SSc Methylation Combined Analysis

## Warning: package 'knitr' was built under R version 3.2.5

1 Part 0: 450K microarray data analysis

1.1 Confirmation of the purified cell type

1.2 PCA of SSc as well as control samples using CD4+ and CD8+ T cells

1.3 Differential Methylation Analysis of CD4+ T cells

1.3.1 Basic Description of CD4+ T cells

[1] "1.Total probes remained: 400420"
[1] "2.Number of the total DMS: 1026"
[1] "3.Number of the hyper DMS: 740"
[1] "4.Number of the hypo DMS: 286"
[1] "5.Number of the genes of the DMS: 621"
[1] "6.Number of the genes of the hyper DMS: 440"
[1] "7.Number of the genes of the hypo DMS: 175"
[1] "8.Number of the genes of the mixed DMS: 6"
[1] "9.Number of the probes located at the promoter: 257"
[1] "10.Number of the genes of the probes located at the promober: 173"
[1] "11.Number of the genes of the hyper probes located at the promober: 117"
[1] "12.Number of the genes of the hypo probes located at the promober: 56"
[1] "13.Number of the genes of the mixed probes located at the promober: 0"

1.4 Differential Methylation Analysis of CD8+ T cells

1.4.1 Basic Description of CD8+ T cells

[1] "1.Total probes remained: 400491"
[1] "2.Number of the total DMS: 2613"
[1] "3.Number of the hyper DMS: 1830"
[1] "4.Number of the hypo DMS: 783"
[1] "5.Number of the genes of the DMS: 1567"
[1] "6.Number of the genes of the hyper DMS: 1086"
[1] "7.Number of the genes of the hypo DMS: 412"
[1] "8.Number of the genes of the mixed DMS: 69"
[1] "9.Number of the probes located at the promoter: 795"
[1] "10.Number of the genes of the probes located at the promober: 500"
[1] "11.Number of the genes of the hyper probes located at the promober: 332"
[1] "12.Number of the genes of the hypo probes located at the promober: 166"
[1] "13.Number of the genes of the mixed probes located at the promober: 2"

1.5 Differential Methylation Analysis of CD4+ and CD8+ T cells

[1] "1.Number of the shared significant CpGsites : 330"
[1] "2.Number of the unique significant CpGsites of CD4+ : 696"
[1] "3.Number of the unique significant CpGsites of CD8+ : 2283"
[1] "4.Number of the shared significant Genes : 215"
[1] "5.The accordance rate of the shared CpGsites: 1.000000"
[1] "6.The number of the hypermethylation genes of the shared Significant CpGsites : 138"
[1] "7.The number of the hypomethylation genes of the shared Significant CpGsites : 75"
[1] "8.The number of the mixed genes of the shared Significant CpGsites : 2"

1.6 Gene Ontology Analysis of CD4+ T cells

GOMFID Pvalue OddsRatio ExpCount Count Size Term
GO:0034340 0.0000054 17.650969 0.4819461 6 25 response to type I interferon
GO:0060337 0.0000054 17.650969 0.4819461 6 25 type I interferon signaling pathway
GO:0048525 0.0001584 11.926537 0.5397797 5 28 negative regulation of viral process
GO:0045071 0.0003135 15.452784 0.3470012 4 18 negative regulation of viral genome replication
GO:0042168 0.0010839 105.049180 0.0578335 2 3 heme metabolic process
GO:0006955 0.0011632 2.768018 7.0749694 16 367 immune response
GO:1903900 0.0012417 7.184664 0.8289474 5 43 regulation of viral life cycle
GO:0051607 0.0012629 5.711434 1.2337821 6 64 defense response to virus
GO:0010288 0.0021408 52.508197 0.0771114 2 4 response to lead ion
GO:0060218 0.0021408 52.508197 0.0771114 2 4 hematopoietic stem cell differentiation
GO:0043903 0.0034670 5.552428 1.0410037 5 54 regulation of symbiosis
GO:0035455 0.0035237 34.994535 0.0963892 2 5 response to interferon-alpha
GO:0033013 0.0052200 26.237705 0.1156671 2 6 tetrapyrrole metabolic process
GO:0045022 0.0052200 26.237705 0.1156671 2 6 early endosome to late endosome transport
GO:0001676 0.0053090 9.965625 0.3662791 3 19 long-chain fatty acid metabolic process
GO:0071345 0.0055523 3.307744 2.7567319 8 143 cellular response to cytokine stimulus
GO:0010970 0.0061608 9.376471 0.3855569 3 20 microtubule-based transport
GO:0002724 0.0072175 20.983607 0.1349449 2 7 regulation of T cell cytokine production
GO:0006950 0.0083516 1.961425 16.0006120 25 830 response to stress

1.7 Gene Ontology Analysis of CD8+ T cells

GOMFID Pvalue OddsRatio ExpCount Count Size Term
GO:0034340 0.0000000 29.711599 0.3162248 7 40 response to type I interferon
GO:0060337 0.0000011 35.017241 0.1919093 5 25 type I interferon signaling pathway
GO:0051607 0.0000246 7.755112 1.2095597 8 153 defense response to virus
GO:0051707 0.0000355 4.470486 3.5180005 13 445 response to other organism
GO:0045071 0.0000397 25.405152 0.1976405 4 25 negative regulation of viral genome replication
GO:0009607 0.0000525 4.291760 3.6523960 13 462 response to biotic stimulus
GO:0008637 0.0000806 12.988782 0.4506203 5 57 apoptotic mitochondrial changes
GO:0090200 0.0001613 35.832845 0.1106787 3 14 positive regulation of release of cytochrome c from mitochondria
GO:0050776 0.0001712 3.780138 4.1030163 13 519 regulation of immune response
GO:2001267 0.0002963 28.144009 0.1343955 3 17 regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:0080134 0.0003352 3.215948 5.6208952 15 711 regulation of response to stress
GO:0045910 0.0003655 129.444444 0.0316225 2 4 negative regulation of DNA recombination
GO:0006955 0.0004375 4.546488 2.3279347 9 339 immune response
GO:0044764 0.0005071 4.019572 2.8697397 10 363 multi-organism cellular process
GO:0048525 0.0005332 12.090909 0.3794697 4 48 negative regulation of viral process
GO:0034341 0.0005619 8.308642 0.6798832 5 86 response to interferon-gamma
GO:0006952 0.0006269 3.154783 5.3443114 14 714 defense response
GO:0002221 0.0008437 7.554307 0.7431282 5 94 pattern recognition receptor signaling pathway
GO:0045132 0.0008478 18.746544 0.1897349 3 24 meiotic chromosome segregation
GO:0044419 0.0008690 3.731350 3.0752858 10 389 interspecies interaction between organisms
GO:0010821 0.0012742 6.852891 0.8142788 5 103 regulation of mitochondrion organization
GO:0035455 0.0016712 43.126984 0.0632450 2 8 response to interferon-alpha
GO:0006733 0.0018775 8.424668 0.5296765 4 67 oxidoreduction coenzyme metabolic process
GO:0060252 0.0021377 36.961451 0.0711506 2 9 positive regulation of glial cell proliferation
GO:0006839 0.0023259 5.932153 0.9328631 5 118 mitochondrial transport
GO:0048678 0.0023692 12.683663 0.2687910 3 34 response to axon injury
GO:0035456 0.0026585 32.337302 0.0790562 2 10 response to interferon-beta
GO:0002830 0.0032328 28.740741 0.0869618 2 11 positive regulation of type 2 immune response
GO:0046597 0.0032328 28.740741 0.0869618 2 11 negative regulation of viral entry into host cell
GO:0050672 0.0032657 11.228571 0.3004135 3 38 negative regulation of lymphocyte proliferation
GO:0048285 0.0034965 3.914005 1.9843104 7 251 organelle fission
GO:1903900 0.0037528 6.880988 0.6403551 4 81 regulation of viral life cycle
GO:0034143 0.0038596 25.863492 0.0948674 2 12 regulation of toll-like receptor 4 signaling pathway
GO:0097296 0.0038596 25.863492 0.0948674 2 12 activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:0007006 0.0040578 10.338285 0.3241304 3 41 mitochondrial membrane organization
GO:0042176 0.0042590 4.287329 1.5415957 6 195 regulation of protein catabolic process
GO:0043068 0.0044008 3.393112 2.6246655 8 332 positive regulation of programmed cell death
GO:0002218 0.0044279 5.066288 1.0830698 5 137 activation of innate immune response
GO:1902589 0.0044799 2.312729 8.7683657 17 1157 single-organism organelle organization
GO:0090025 0.0045382 23.509380 0.1027730 2 13 regulation of monocyte chemotaxis
GO:2000377 0.0050479 6.302108 0.6956945 4 88 regulation of reactive oxygen species metabolic process
GO:0071345 0.0050763 3.307969 2.6879105 8 340 cellular response to cytokine stimulus
GO:2000108 0.0052677 21.547619 0.1106787 2 14 positive regulation of leukocyte apoptotic process
GO:0030260 0.0052817 9.349078 0.3557529 3 45 entry into host cell
GO:0051828 0.0052817 9.349078 0.3557529 3 45 entry into other organism involved in symbiotic interaction
GO:0052126 0.0052817 9.349078 0.3557529 3 45 movement in host environment
GO:0032102 0.0054658 4.806954 1.1384091 5 144 negative regulation of response to external stimulus
GO:0034138 0.0056186 9.130533 0.3636585 3 46 toll-like receptor 3 signaling pathway
GO:0009895 0.0056846 6.082533 0.7194113 4 91 negative regulation of catabolic process
GO:0043123 0.0059082 6.012668 0.7273170 4 92 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0060338 0.0060472 19.887668 0.1185843 2 15 regulation of type I interferon-mediated signaling pathway
GO:0050727 0.0061308 4.670163 1.1700316 5 148 regulation of inflammatory response
GO:0031349 0.0063777 3.925127 1.6759912 6 212 positive regulation of defense response
GO:0042981 0.0064414 2.443857 6.0873267 13 770 regulation of apoptotic process
GO:0002507 0.0068761 18.464853 0.1264899 2 16 tolerance induction
GO:0007129 0.0068761 18.464853 0.1264899 2 16 synapsis
GO:0010939 0.0068761 18.464853 0.1264899 2 16 regulation of necrotic cell death
GO:0031338 0.0068761 18.464853 0.1264899 2 16 regulation of vesicle fusion
GO:0006974 0.0070974 3.407861 2.2610071 7 286 cellular response to DNA damage stimulus
GO:0032103 0.0072326 4.478747 1.2174653 5 154 positive regulation of response to external stimulus
GO:0016601 0.0077534 17.231746 0.1343955 2 17 Rac protein signal transduction
GO:0045646 0.0077534 17.231746 0.1343955 2 17 regulation of erythrocyte differentiation
GO:0000710 0.0079056 Inf 0.0079056 1 1 meiotic mismatch repair
GO:0005999 0.0079056 Inf 0.0079056 1 1 xylulose biosynthetic process
GO:0009052 0.0079056 Inf 0.0079056 1 1 pentose-phosphate shunt
GO:0010266 0.0079056 Inf 0.0079056 1 1 response to vitamin B1
GO:0014739 0.0079056 Inf 0.0079056 1 1 positive regulation of muscle hyperplasia
GO:0015747 0.0079056 Inf 0.0079056 1 1 urate transport
GO:0034127 0.0079056 Inf 0.0079056 1 1 regulation of MyD88-independent toll-like receptor signaling pathway
GO:0034157 0.0079056 Inf 0.0079056 1 1 positive regulation of toll-like receptor 7 signaling pathway
GO:0034165 0.0079056 Inf 0.0079056 1 1 positive regulation of toll-like receptor 9 signaling pathway
GO:0034276 0.0079056 Inf 0.0079056 1 1 kynurenic acid biosynthetic process
GO:0036269 0.0079056 Inf 0.0079056 1 1 swimming behavior
GO:0038195 0.0079056 Inf 0.0079056 1 1 urokinase plasminogen activator signaling pathway
GO:0042795 0.0079056 Inf 0.0079056 1 1 snRNA transcription from RNA polymerase II promoter
GO:0044727 0.0079056 Inf 0.0079056 1 1 DNA demethylation of male pronucleus
GO:0048294 0.0079056 Inf 0.0079056 1 1 negative regulation of isotype switching to IgE isotypes
GO:0070447 0.0079056 Inf 0.0079056 1 1 positive regulation of oligodendrocyte progenitor proliferation
GO:0070667 0.0079056 Inf 0.0079056 1 1 negative regulation of mast cell proliferation
GO:0072046 0.0079056 Inf 0.0079056 1 1 establishment of planar polarity involved in nephron morphogenesis
GO:0090220 0.0079056 Inf 0.0079056 1 1 chromosome localization to nuclear envelope involved in homologous chromosome segregation
GO:0090258 0.0079056 Inf 0.0079056 1 1 negative regulation of mitochondrial fission
GO:1900402 0.0079056 Inf 0.0079056 1 1 regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter
GO:1902616 0.0079056 Inf 0.0079056 1 1 acyl carnitine transmembrane transport
GO:1903147 0.0079056 Inf 0.0079056 1 1 negative regulation of mitophagy
GO:1903852 0.0079056 Inf 0.0079056 1 1 positive regulation of cristae formation
GO:1904379 0.0079056 Inf 0.0079056 1 1 protein localization to cytosolic proteasome complex involved in ERAD pathway
GO:1904544 0.0079056 Inf 0.0079056 1 1 positive regulation of free ubiquitin chain polymerization
GO:0007059 0.0079113 5.506147 0.7905619 4 100 chromosome segregation
GO:0050869 0.0086783 16.152778 0.1423011 2 18 negative regulation of B cell activation
GO:0001817 0.0092878 3.227832 2.3795913 7 301 regulation of cytokine production
GO:0051603 0.0093687 3.601544 1.8182924 6 230 proteolysis involved in cellular protein catabolic process
GO:0050863 0.0096005 4.165104 1.3044271 5 165 regulation of T cell activation
GO:0043903 0.0096766 5.178399 0.8379956 4 106 regulation of symbiosis
GO:0051716 0.0098518 1.852192 29.1638288 39 3689 cellular response to stimulus

2 Part 1: MethylTarget Technology Evaluation and Quality Control

2.1 Quality Control:The average coverage of each sample, each CpGsite, and each gene (average coverage of the CpGsites in a gene)

2.1.1 Table 1: The Average Missing Rate of Each Sample

Sample Missing.Rate
D10 D10 0.173
D11 D11 0.173
D12 D12 0.132
D13 D13 0.173
D14 D14 0.173
D15 D15 0.173
D1 D1 0.173
D2 D2 0.173
D3 D3 0.173
D4 D4 0.173
D5 D5 0.173
D6 D6 0.173
D7 D7 0.173
D8 D8 0.132
D9 D9 0.173
MS001 MS001 0.132
MS002 MS002 0.148
MS003 MS003 0.132
MS004 MS004 0.132
MS005 MS005 0.132
MS006 MS006 0.132
MS007 MS007 0.132
MS008 MS008 0.132
MS009 MS009 0.132
MS010 MS010 0.132
MS011 MS011 0.136
MS012 MS012 0.132
MS013 MS013 0.132
MS014 MS014 0.136
MS015 MS015 0.169
MS016 MS016 0.148
MS017 MS017 0.169
MS018 MS018 0.132
MS019 MS019 0.132
MS020 MS020 0.132
MS021 MS021 0.132
MS022 MS022 0.132
MS023 MS023 0.132
MS024 MS024 0.000
MS025 MS025 0.132
MS026 MS026 0.132
MS027 MS027 0.132
MS028 MS028 0.132
MS029 MS029 0.132
MS030 MS030 0.132
MS031 MS031 0.132
MS032 MS032 0.132
MS033 MS033 0.132
MS034 MS034 0.132
MS035 MS035 0.132
MS036 MS036 0.132
MS037 MS037 0.132
MS038 MS038 0.132
MS039 MS039 0.193
MS040 MS040 0.132
MS041 MS041 0.152
MS042 MS042 0.132
MS043 MS043 0.132
MS044 MS044 0.148
MS045 MS045 0.132
MS046 MS046 0.140
MS047 MS047 0.165
MS048 MS048 0.132
MS049 MS049 0.132
MS050 MS050 0.132
MS051 MS051 0.136
MS052 MS052 0.132
MS053 MS053 0.132
MS054 MS054 0.148
MS055 MS055 0.132
MS056 MS056 0.169
MS057 MS057 0.132
MS058 MS058 0.148
MS059 MS059 0.132
MS060 MS060 0.132
MS061 MS061 0.132
MS062 MS062 0.000
MS063 MS063 0.132
MS064 MS064 0.132
MS065 MS065 0.132
MS066 MS066 0.132
MS067 MS067 0.214
MS068 MS068 0.132
MS069 MS069 0.132
MS070 MS070 0.165
MS071 MS071 0.132
MS072 MS072 0.486
MS073 MS073 0.132
MS074 MS074 0.132
MS075 MS075 0.132
MS076 MS076 0.132
MS077 MS077 0.148
MS078 MS078 0.132
MS079 MS079 0.132
MS080 MS080 0.136
MS081 MS081 0.148
MS082 MS082 0.156
MS083 MS083 0.169
MS084 MS084 0.132
MS085 MS085 0.132
MS086 MS086 0.132
MS087 MS087 0.276
MS088 MS088 0.132
MS089 MS089 0.132
MS090 MS090 0.132
MS091 MS091 0.132
MS092 MS092 0.132
MS093 MS093 0.144
MS094 MS094 0.136
MS095 MS095 0.132
MS096 MS096 0.148
MS097 MS097 0.132
MS098 MS098 0.119
MS099 MS099 0.169
MS100 MS100 0.136
MS101 MS101 0.136
MS102 MS102 0.148
MS103 MS103 0.132
MS104 MS104 0.588
MS105 MS105 0.136
MS106 MS106 0.132
MS107 MS107 0.132
MS108 MS108 0.218
MS109 MS109 0.132
MS110 MS110 0.132
MS111 MS111 0.132
MS112 MS112 0.132
MS113 MS113 0.132
MS114 MS114 0.132
MS115 MS115 0.148
MS116 MS116 0.251
MS117 MS117 0.136
MS118 MS118 0.132
MS119 MS119 0.136
MS120 MS120 0.132
MS121 MS121 0.136
MS122 MS122 0.132
MS123 MS123 0.218
MS124 MS124 0.440
MS125 MS125 0.132
MS126 MS126 0.140
MS127 MS127 0.132
MS128 MS128 0.132
MS129 MS129 0.132
MS130 MS130 0.132
MS131 MS131 0.132
MS132 MS132 0.132
MS133 MS133 0.132
MS134 MS134 0.132
MS135 MS135 0.132
MS136 MS136 0.144
MS137 MS137 0.132
MS138 MS138 0.132
MS139 MS139 0.132
MS140 MS140 0.132
MS141 MS141 0.132
MS142 MS142 0.148
MS143 MS143 0.132
MS144 MS144 0.132
MS145 MS145 0.132
MS146 MS146 0.148
MS147 MS147 0.136
MS148 MS148 0.136
MS149 MS149 0.132
MS150 MS150 0.136
MS151 MS151 0.251
MS152 MS152 0.140
MS153 MS153 0.148
MS154 MS154 0.132
MS155 MS155 0.132
MS156 MS156 0.132
MS157 MS157 0.144
MS158 MS158 0.251
MS159 MS159 0.132
MS160 MS160 0.132
MS161 MS161 0.140
MS162 MS162 0.235
MS163 MS163 0.202
MS164 MS164 0.185

2.1.2 Table 2: The Average Coverage of Each CpGsite

Gene Total.CpG Avg.Coverage
MX1 42798695 1617.089385
MX1 42798698 1617.100559
MX1 42798723 1617.117318
MX1 42798733 1617.111732
MX1 42798747 1617.737430
MX1 42798749 1618.491620
MX1 42798765 1623.603352
MX1 42798781 1623.675978
MX1 42798813 1620.921788
MX1 42798816 1619.284916
MX1 42798818 1618.072626
MX1 42798829 1617.100559
MX1 42798837 1617.100559
MX1 42798847 1617.089385
MX1 42798857 1617.083799
MX1 42798863 1617.061453
CCDC85C 100069535 2.308943
CCDC85C 100069538 2.308943
CCDC85C 100069541 2.308943
CCDC85C 100069544 2.308943
CCDC85C 100069552 2.317073
CCDC85C 100069563 2.317073
CCDC85C 100069566 2.317073
CCDC85C 100069585 2.325203
CCDC85C 100069588 2.325203
CCDC85C 100069601 2.325203
CCDC85C 100069606 2.325203
CCDC85C 100069619 2.365854
CCDC85C 100069630 2.782258
CCDC85C 100069645 2.801587
CCDC85C 100069654 2.547619
CCDC85C 100069657 2.357143
CCDC85C 100069664 2.349206
CCDC85C 100069666 2.349206
CCDC85C 100069673 2.349206
CCDC85C 100069684 2.349206
CCDC85C 100069687 2.349206
CCDC85C 100069693 2.349206
CCDC85C 100069696 2.349206
CCDC85C 100069698 2.349206
CCDC85C 100069706 2.349206
CCDC85C 100069708 2.349206
CCDC85C 100069711 2.349206
CCDC85C 100069715 2.349206
CCDC85C 100069717 2.349206
CCDC85C 100069724 2.349206
CCDC85C 100069730 2.349206
CCDC85C 100069735 2.349206
RNF39 30039123 210.497207
RNF39 30039127 210.709497
RNF39 30039130 210.804469
RNF39 30039132 210.860335
RNF39 30039142 210.921788
RNF39 30039151 210.927374
RNF39 30039158 210.932961
RNF39 30039175 210.944134
RNF39 30039186 210.938547
RNF39 30039202 210.938547
RNF39 30039206 210.932961
RNF39 30039208 210.944134
RNF39 30039232 210.463687
RNF39 30039235 209.972067
RNF39 30039239 209.703911
COX7A2 75953821 2134.955056
COX7A2 75953829 2134.966292
COX7A2 75953853 2134.966292
COX7A2 75953883 2140.500000
COX7A2 75953935 2135.028090
COX7A2 75953937 2135.000000
COX7A2 75953960 2134.983146
COX7A2 75953974 2134.983146
SMAD3 67361773 126.500000
SMAD3 67361798 126.516854
SMAD3 67361821 126.741573
SMAD3 67361896 126.511236
HLA-DPB1 33048286 965.536313
HLA-DPB1 33048291 965.541899
HLA-DPB1 33048310 965.558659
HLA-DPB1 33048370 965.547486
RNF39 30039271 155.005587
RNF39 30039274 155.000000
RNF39 30039278 155.000000
RNF39 30039303 155.000000
RNF39 30039307 155.000000
RNF39 30039313 155.000000
RNF39 30039323 155.000000
RNF39 30039349 154.988827
RNF39 30039354 155.273743
RNF39 30039364 155.798883
RNF39 30039374 155.877095
RNF39 30039376 155.871508
RNF39 30039380 155.843575
RNF39 30039403 154.949721
RNF39 30039408 154.983240
RNF39 30039411 154.949721
RNF39 30039415 154.955307
RNF39 30039418 154.949721
RNF39 30039432 154.955307
RNF39 30039435 154.960894
RNF39 30039442 154.949721
RNF39 30039466 154.949721
RNF39 30039476 154.698324
TTC39C 21572657 6267.117318
TTC39C 21572635 6267.000000
TTC39C 21572623 6266.988827
IFITM1 313354 302.402235
IFITM1 313408 302.340782
HOOK2 12877099 1991.089385
HOOK2 12877107 1991.089385
HOOK2 12877138 1991.167598
HOOK2 12877188 2003.675978
HOOK2 12877201 2003.648045
HOOK2 12877215 1991.396648
HOOK2 12877235 1990.960894
HOOK2 12877276 1990.899441
PARP9 122281939 1402.916201
PARP9 122281975 1403.078212
BRDT 92414650 272.357542
BRDT 92414661 272.357542
BRDT 92414719 273.089385
BRDT 92414722 273.072626
BRDT 92414737 273.072626
BRDT 92414751 273.016760
BRDT 92414770 272.379888
BRDT 92414782 272.379888
BRDT 92414793 272.379888
COX7A2 75954022 466.061452
COX7A2 75954053 466.111732
COX7A2 75954118 466.044693
COX7A2 75954122 465.977654
HELZ2 62199034 118.670455
HELZ2 62199061 118.670455
HELZ2 62199156 118.676136
HELZ2 62199181 118.676136
HELZ2 62199190 118.670455
GFPT2 179741121 795.642458
GFPT2 179741105 796.826816
GFPT2 179741101 797.603352
GFPT2 179741081 795.843575
GFPT2 179741067 795.921788
GFPT2 179741063 795.793296
GFPT2 179741060 795.793296
GFPT2 179741042 745.469274
GFPT2 179741039 718.039106
EIF2AK2 37383568 1496.245810
EIF2AK2 37383588 1496.279330
EIF2AK2 37383623 1498.664804
EIF2AK2 37383679 1496.301676
EIF2AK2 37383713 1496.318436
EIF2AK2 37383730 1496.318436
TLR1 38805732 33.642046
TLR1 38805839 33.653409
HOOK2 12877020 5503.972067
HOOK2 12877001 5545.195531
HOOK2 12876997 5545.642458
HOOK2 12876993 5545.178771
HOOK2 12876987 5545.162011
HOOK2 12876969 5545.167598
HOOK2 12876948 5547.832402
HOOK2 12876946 5545.245810
HOOK2 12876944 5545.167598
HOOK2 12876942 5545.229050
HOOK2 12876937 5545.178771
HOOK2 12876926 5542.759777
HOOK2 12876918 5534.843575
HOOK2 12876911 5508.072626
GFPT2 179741008 1613.100559
GFPT2 179740999 1613.815642
GFPT2 179740994 1613.821229
GFPT2 179740992 1613.826816
GFPT2 179740970 1613.821229
GFPT2 179740963 1613.821229
GFPT2 179740957 1613.826816
GFPT2 179740955 1613.832402
GFPT2 179740940 1615.620112
GFPT2 179740935 1615.893855
GFPT2 179740920 1616.173184
GFPT2 179740918 1616.184358
GFPT2 179740915 1616.162011
GFPT2 179740906 1616.178771
GFPT2 179740900 1616.117318
GFPT2 179740888 1615.368715
GFPT2 179740869 1613.854749
GFPT2 179740867 1613.810056
GFPT2 179740861 1613.815642
GFPT2 179740855 1613.893855
GFPT2 179740852 1613.815642
GFPT2 179740840 1613.798883
GFPT2 179740832 1613.793296
GFPT2 179740825 1613.854749
GFPT2 179740822 1613.804469
FAM132A 1178246 634.519553
FAM132A 1178207 634.614525
FAM132A 1178202 635.653631
FAM132A 1178192 636.011173
FAM132A 1178182 636.329609
FAM132A 1178172 636.363129
FAM132A 1178162 635.748603
FAM132A 1178150 634.832402
FAM132A 1178136 634.832402
FAM132A 1178118 634.837989
FAM132A 1178105 634.843575
FAM132A 1178086 634.832402
BRDT 92417998 722.083799
BRDT 92418017 722.078212
HLA-DPB1 33048417 273.307263
HLA-DPB1 33048423 273.312849
HLA-DPB1 33048433 273.318436
HLA-DPB1 33048444 273.351955
HLA-DPB1 33048469 273.324022
HLA-DPB1 33048483 273.513966
HLA-DPB1 33048485 273.625698
HLA-DPB1 33048502 274.798883
HLA-DPB1 33048529 274.089385
HLA-DPB1 33048540 273.329609
HLA-DPB1 33048542 273.324022
HLA-DPB1 33048544 273.324022
HLA-DPB1 33048549 273.324022
HLA-DPB1 33048555 273.324022
HLA-DPB1 33048558 273.324022
HLA-DPB1 33048571 273.346369
HLA-DPB1 33048575 273.329609
HLA-DPB1 33048581 273.312849
HLA-DPB1 33048592 273.318436
HLA-DPB1 33048602 273.307263
IFI44L 79085586 465.646067
IFI44L 79085647 465.646067
IFI44L 79085713 465.640449
IFI44L 79085765 465.640449
IFITM1 312419 71.934524
IFITM1 312434 74.345238
IFITM1 312463 85.023809
IFITM1 312518 57.890909
UPK3B 76145717 831.505882
UPK3B 76145702 832.070588
UPK3B 76145693 834.358823
UPK3B 76145689 834.741177
UPK3B 76145673 835.000000
UPK3B 76145633 834.988235
UPK3B 76145628 834.988235
UPK3B 76145620 834.982353
UPK3B 76145606 834.982353
UPK3B 76145589 832.070588
###Table 3: The Average C overage of Each Gene
Gene Average Coverage of Gene
2 CCDC85C 2.372799
16 TLR1 33.647727
7 HELZ2 118.672727
15 SMAD3 126.567416
11 IFITM1 148.989583
14 RNF39 177.064540
1 BRDT 354.388014
8 HLA-DPB1 388.807961
10 IFI44L 465.643258
5 FAM132A 635.284916
18 UPK3B 833.968823
6 GFPT2 1394.086428
13 PARP9 1402.997207
4 EIF2AK2 1496.688082
3 COX7A2 1579.131463
12 MX1 1618.477654
9 HOOK2 4249.935246
17 TTC39C 6267.035382

2.2 Correlation of MethylTarget Technology and Methylation 450K technology with same samples and same CpGsites in CD4+/CD8+

2.2.1 Table 4: The Correlation of each CpGsite between two techniques in CD4+ and CD8+ T cells

CpGsites Position Gene Cor Cor.p
cg08924203 cg08924203 42798747 MX1 0.7875911 0.0000000
cg09234582 cg09234582 33048286 HLA-DPB1 0.8329984 0.0000000
cg25045942 cg25045942 33048291 HLA-DPB1 0.8769142 0.0000000
cg13349035 cg13349035 33048310 HLA-DPB1 0.8813230 0.0000000
cg24961286 cg24961286 67361773 SMAD3 0.9302960 0.0000000
cg06809298 cg06809298 75953853 COX7A2 0.9400949 0.0000000
cg19367436 cg19367436 75953935 COX7A2 0.8163266 0.0000000
cg00947782 cg00947782 30039142 RNF39 0.5845140 0.0000103
cg18930910 cg18930910 30039151 RNF39 0.5916786 0.0000076
cg03343571 cg03343571 30039175 RNF39 0.5276578 0.0000978
cg20249327 cg20249327 30039374 RNF39 0.9220030 0.0000000
cg15877520 cg15877520 30039376 RNF39 0.9296247 0.0000000
cg13918754 cg13918754 30039380 RNF39 0.9596576 0.0000000
cg09279736 cg09279736 30039403 RNF39 0.9135974 0.0000000
cg07382347 cg07382347 30039408 RNF39 0.9166788 0.0000000
cg13401893 cg13401893 30039432 RNF39 0.9084653 0.0000000
cg12633154 cg12633154 30039435 RNF39 0.8883291 0.0000000
cg10568066 cg10568066 30039442 RNF39 0.8677459 0.0000000
cg16078649 cg16078649 30039466 RNF39 0.9190687 0.0000000
cg10930308 cg10930308 30039476 RNF39 0.9493699 0.0000000
cg11694510 cg11694510 313354 IFITM1 0.7864492 0.0000000
cg23899408 cg23899408 12877188 HOOK2 0.9765644 0.0000000
cg14732540 cg14732540 92414722 BRDT 0.8713379 0.0000000
cg13299824 cg13299824 92414737 BRDT 0.8400119 0.0000000
cg02935097 cg02935097 92414782 BRDT 0.7988980 0.0000000
cg08122652 cg08122652 122281939 PARP9 0.7637794 0.0000000
cg00959259 cg00959259 122281975 PARP9 0.6588623 0.0000003
cg25716013 cg25716013 75954053 COX7A2 0.9095258 0.0000000
cg17593958 cg17593958 62199034 HELZ2 0.8444909 0.0000000
cg11779113 cg11779113 62199156 HELZ2 0.4249446 0.0040367
cg06064964 cg06064964 62199181 HELZ2 0.7381923 0.0000000
cg09844573 cg09844573 62199190 HELZ2 0.6197099 0.0000073
cg17326313 cg17326313 37383568 EIF2AK2 0.8792872 0.0000000
cg02016764 cg02016764 38805732 TLR1 0.7114730 0.0000008
cg01081438 cg01081438 92417998 BRDT 0.9337179 0.0000000
cg10850215 cg10850215 33048469 HLA-DPB1 0.6474086 0.0000007
cg03229061 cg03229061 33048483 HLA-DPB1 0.4858796 0.0004636
cg17588455 cg17588455 33048485 HLA-DPB1 0.7545157 0.0000000
cg26645432 cg26645432 33048502 HLA-DPB1 0.1232234 0.4040559
cg06437840 cg06437840 33048529 HLA-DPB1 0.7110659 0.0000000
cg14870156 cg14870156 33048540 HLA-DPB1 0.0343315 0.8168069
cg19990651 cg19990651 33048555 HLA-DPB1 0.7052687 0.0000000
cg01132696 cg01132696 33048558 HLA-DPB1 0.3265685 0.0234882
cg03607951 cg03607951 79085586 IFI44L 0.6966504 0.0000000
cg17980508 cg17980508 79085713 IFI44L 0.6256915 0.0000020
cg00855901 cg00855901 79085765 IFI44L 0.7205904 0.0000000
cg05432003 cg05432003 312518 IFITM1 0.0566625 0.8022332
cg05372444 cg05372444 76145673 UPK3B 0.0945557 0.5181153
cg16453056 cg16453056 76145633 UPK3B -0.0627056 0.6686297
cg18719665 cg18719665 21572657 TTC39C 0.7129571 0.0000000
cg05401069 cg05401069 21572635 TTC39C 0.7021158 0.0000000
cg12639429 cg12639429 21572623 TTC39C 0.7214840 0.0000000
cg02891314 cg02891314 179741121 GFPT2 0.9772109 0.0000000
cg23248424 cg23248424 179741105 GFPT2 0.9740999 0.0000000
cg11738485 cg11738485 12877001 HOOK2 0.9661724 0.0000000
cg13944838 cg13944838 179740915 GFPT2 0.9192473 0.0000000
cg24345856 cg24345856 1178246 FAM132A 0.9772829 0.0000000

2.2.2 Table 5: The Correlation of each CpGsite between two techniques in CD4+ T cells

CpGsites Gene Cor Cor.p
cg08924203 cg08924203 MX1 0.8299157 0.0000003
cg09234582 cg09234582 HLA-DPB1 0.8654015 0.0000000
cg25045942 cg25045942 HLA-DPB1 0.8925666 0.0000000
cg13349035 cg13349035 HLA-DPB1 0.9083435 0.0000000
cg24961286 cg24961286 SMAD3 0.9460214 0.0000000
cg06809298 cg06809298 COX7A2 0.9589386 0.0000000
cg19367436 cg19367436 COX7A2 0.8566601 0.0000001
cg00947782 cg00947782 RNF39 0.6241475 0.0008548
cg18930910 cg18930910 RNF39 0.5285853 0.0065991
cg03343571 cg03343571 RNF39 0.5337884 0.0059928
cg20249327 cg20249327 RNF39 0.9182796 0.0000000
cg15877520 cg15877520 RNF39 0.9374247 0.0000000
cg13918754 cg13918754 RNF39 0.9548662 0.0000000
cg09279736 cg09279736 RNF39 0.9228781 0.0000000
cg07382347 cg07382347 RNF39 0.9244311 0.0000000
cg13401893 cg13401893 RNF39 0.9082009 0.0000000
cg12633154 cg12633154 RNF39 0.9102277 0.0000000
cg10568066 cg10568066 RNF39 0.8987335 0.0000000
cg16078649 cg16078649 RNF39 0.9467700 0.0000000
cg10930308 cg10930308 RNF39 0.9551814 0.0000000
cg11694510 cg11694510 IFITM1 0.7563685 0.0000122
cg23899408 cg23899408 HOOK2 0.9775041 0.0000000
cg14732540 cg14732540 BRDT 0.8203313 0.0000005
cg13299824 cg13299824 BRDT 0.8513942 0.0000001
cg02935097 cg02935097 BRDT 0.8637596 0.0000000
cg08122652 cg08122652 PARP9 0.7920321 0.0000024
cg00959259 cg00959259 PARP9 0.7744853 0.0000055
cg25716013 cg25716013 COX7A2 0.8931213 0.0000000
cg17593958 cg17593958 HELZ2 0.7961157 0.0000158
cg11779113 cg11779113 HELZ2 0.3829578 0.0866200
cg06064964 cg06064964 HELZ2 0.7340518 0.0001519
cg09844573 cg09844573 HELZ2 0.6369182 0.0019033
cg17326313 cg17326313 EIF2AK2 0.9105197 0.0000000
cg02016764 cg02016764 TLR1 0.6434139 0.0006942
cg01081438 cg01081438 BRDT 0.9408440 0.0000000
cg10850215 cg10850215 HLA-DPB1 0.7368557 0.0000266
cg03229061 cg03229061 HLA-DPB1 0.4504181 0.0238546
cg17588455 cg17588455 HLA-DPB1 0.8114746 0.0000009
cg26645432 cg26645432 HLA-DPB1 0.2312224 0.2661047
cg06437840 cg06437840 HLA-DPB1 0.7226194 0.0000451
cg14870156 cg14870156 HLA-DPB1 -0.0263505 0.9005009
cg19990651 cg19990651 HLA-DPB1 0.7628868 0.0000092
cg01132696 cg01132696 HLA-DPB1 0.2636762 0.2028171
cg03607951 cg03607951 IFI44L 0.5938188 0.0022188
cg17980508 cg17980508 IFI44L 0.4851683 0.0162569
cg00855901 cg00855901 IFI44L 0.5496102 0.0054020
cg05432003 cg05432003 IFITM1 0.2915337 0.4835571
cg05372444 cg05372444 UPK3B 0.1231249 0.5576437
cg16453056 cg16453056 UPK3B -0.1314347 0.5311479
cg18719665 cg18719665 TTC39C 0.7752723 0.0000053
cg05401069 cg05401069 TTC39C 0.8837758 0.0000000
cg12639429 cg12639429 TTC39C 0.8685243 0.0000000
cg02891314 cg02891314 GFPT2 0.9830951 0.0000000
cg23248424 cg23248424 GFPT2 0.9803569 0.0000000
cg11738485 cg11738485 HOOK2 0.9654121 0.0000000
cg13944838 cg13944838 GFPT2 0.9162778 0.0000000
cg24345856 cg24345856 FAM132A 0.9758109 0.0000000

2.2.3 Table 6: The Correlation of each CpGsite between two techniques in CD8+ T cells

CpGsites Gene Cor Cor.p
cg08924203 cg08924203 MX1 0.8415787 0.0000001
cg00947782 cg00947782 RNF39 0.6452495 0.0006624
cg18930910 cg18930910 RNF39 0.6936552 0.0001707
cg03343571 cg03343571 RNF39 0.6162826 0.0013425
cg09234582 cg09234582 HLA-DPB1 0.7949194 0.0000021
cg25045942 cg25045942 HLA-DPB1 0.8763508 0.0000000
cg13349035 cg13349035 HLA-DPB1 0.8666077 0.0000000
cg06809298 cg06809298 COX7A2 0.9425910 0.0000000
cg19367436 cg19367436 COX7A2 0.8157639 0.0000012
cg20249327 cg20249327 RNF39 0.9287367 0.0000000
cg15877520 cg15877520 RNF39 0.9228730 0.0000000
cg13918754 cg13918754 RNF39 0.9738624 0.0000000
cg09279736 cg09279736 RNF39 0.9528922 0.0000000
cg07382347 cg07382347 RNF39 0.9573280 0.0000000
cg13401893 cg13401893 RNF39 0.9167430 0.0000000
cg12633154 cg12633154 RNF39 0.8927020 0.0000000
cg10568066 cg10568066 RNF39 0.8855962 0.0000000
cg16078649 cg16078649 RNF39 0.9116806 0.0000000
cg10930308 cg10930308 RNF39 0.9483145 0.0000000
cg11694510 cg11694510 IFITM1 0.8453997 0.0000002
cg23899408 cg23899408 HOOK2 0.9768685 0.0000000
cg25716013 cg25716013 COX7A2 0.9555204 0.0000000
cg14732540 cg14732540 BRDT 0.9358410 0.0000000
cg13299824 cg13299824 BRDT 0.9490383 0.0000000
cg02935097 cg02935097 BRDT 0.9521191 0.0000000
cg17593958 cg17593958 HELZ2 0.9401700 0.0000000
cg11779113 cg11779113 HELZ2 0.5030812 0.0144080
cg06064964 cg06064964 HELZ2 0.7573440 0.0000286
cg09844573 cg09844573 HELZ2 0.5751135 0.0040931
cg08122652 cg08122652 PARP9 0.7913177 0.0000041
cg00959259 cg00959259 PARP9 0.6063288 0.0016849
cg17326313 cg17326313 EIF2AK2 0.8385426 0.0000003
cg02016764 cg02016764 TLR1 0.9051719 0.0000209
cg01081438 cg01081438 BRDT 0.9295378 0.0000000
cg10850215 cg10850215 HLA-DPB1 0.5787968 0.0038085
cg03229061 cg03229061 HLA-DPB1 0.5742491 0.0041624
cg17588455 cg17588455 HLA-DPB1 0.6503313 0.0007807
cg26645432 cg26645432 HLA-DPB1 -0.1544432 0.4816708
cg06437840 cg06437840 HLA-DPB1 0.6946460 0.0002351
cg14870156 cg14870156 HLA-DPB1 0.1173008 0.5940133
cg19990651 cg19990651 HLA-DPB1 0.5971490 0.0026261
cg01132696 cg01132696 HLA-DPB1 0.4154478 0.0486716
cg03607951 cg03607951 IFI44L 0.8475412 0.0000002
cg17980508 cg17980508 IFI44L 0.8752929 0.0000000
cg00855901 cg00855901 IFI44L 0.9405970 0.0000000
cg05432003 cg05432003 IFITM1 -0.0256578 0.9306198
cg24961286 cg24961286 SMAD3 0.9522798 0.0000000
cg05372444 cg05372444 UPK3B 0.0752061 0.7268941
cg16453056 cg16453056 UPK3B -0.0248870 0.9081045
cg18719665 cg18719665 TTC39C 0.9106746 0.0000000
cg05401069 cg05401069 TTC39C 0.9321970 0.0000000
cg12639429 cg12639429 TTC39C 0.9401501 0.0000000
cg02891314 cg02891314 GFPT2 0.9790054 0.0000000
cg23248424 cg23248424 GFPT2 0.9675930 0.0000000
cg11738485 cg11738485 HOOK2 0.9689259 0.0000000
cg13944838 cg13944838 GFPT2 0.9249767 0.0000000
cg24345856 cg24345856 FAM132A 0.9804414 0.0000000

2.2.4 Figure1: The Correlation of all CpGsites between two techniques in CD4+ T cells

[1] "The Correlation r^2 of the two techniques in CD4+ T cells is 0.861615"

2.2.5 Figure2: The Correlation of all CpGsites between two techniques in CD8+ T cells

[1] "The Correlation r^2 of the two techniques in CD8+ T cells is 0.898798"

2.2.6 Figure3: The Correlation of all CpGsites between two techniques in CD4+ and CD8+ T cells

[1] "The Correlation r^2 of the two techniques in CD4+ and CD8+ T cells is 0.879452"

2.2.7 Figure4 : The correlation between the correlation r^2 and coverage depth

2.3 Part I Summary:

In Part I, we conducted several quality control analysis to reveal the quality of NGS sequencing validation data, and compared it with the DNA methylation 450K datasets with the same CpGsites and same samples. And we found that the correlation of the two techniques is relatively good and showed no difference between CD4+ and CD8+ T cells, indicating its unbiased characteristics. Also, we found that the NGS sequencing depth is very high, with mean depth reached nearly 1000x, indicating its robustness for methylation status detection. In conclusion, we found the bisulfite sequencing with high coverage is a robust method for methylation status detection and showed strong linear correlation with the results came from DNA methylation 450K microarry datasets. Thus we can safely use the results of the bisulfite sequencing data for our further analysis.

3 Part II: Validation of differential methylated CpGsites with MethylTarget technology

3.1 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD4+

3.1.1 Validation of differential methylated CpGsites between SSc patients and Controls

3.1.1.1 Table 7: The Differential methylated CpGsites between SSc patients and Controls

Gene Pos Mean.CD4.SSc Mean.CD4.NC P.value.CD4.SSC.NC FDR Cgname
38 EIF2AK2 37383568 0.1233814 0.1826725 0.0000315 0.0017293 cg17326313
27 PARP9 122281975 0.4276390 0.5290290 0.0000693 0.0017293 cg00959259
52 IFI44L 79085586 0.6726998 0.7436687 0.0000910 0.0017293 cg03607951
24 IFITM1 313354 0.2627358 0.3098730 0.0011124 0.0158510 cg11694510
26 PARP9 122281939 0.7183252 0.7916144 0.0015986 0.0182241 cg08122652
1 MX1 42798747 0.0572312 0.0650165 0.0024990 0.0237408 cg08924203
34 HELZ2 62199181 0.0651395 0.0373344 0.0055478 0.0451752 cg06064964
43 BRDT 92417998 0.4365022 0.3211686 0.0259938 0.1852058 cg01081438
54 IFI44L 79085765 0.4548280 0.4984651 0.0311206 0.1970972 cg00855901
42 FAM132A 1178246 0.7422693 0.8213389 0.0357950 0.1996182 cg24345856
30 BRDT 92414782 0.7324310 0.7659456 0.0385228 0.1996182 cg02935097
33 HELZ2 62199156 0.0326060 0.0191877 0.0515001 0.2446256 cg11779113
32 HELZ2 62199034 0.1286726 0.0909342 0.0741810 0.3252549 cg17593958
49 HLA-DPB1 33048540 0.8897127 0.9221222 0.0855347 0.3482483 cg14870156
53 IFI44L 79085713 0.6427472 0.6830388 0.1218293 0.4629515 cg17980508
29 BRDT 92414737 0.5443314 0.5645251 0.1433180 0.4913739 cg13299824
19 RNF39 30039466 0.2044569 0.2484926 0.1550571 0.4913739 cg16078649
47 HLA-DPB1 33048502 0.9067644 0.9422507 0.1610061 0.4913739 cg26645432
28 BRDT 92414722 0.3656732 0.3848972 0.1637913 0.4913739 cg14732540
13 RNF39 30039380 0.2090533 0.2633600 0.1855721 0.5288806 cg13918754
35 HELZ2 62199190 0.0445401 0.0314240 0.2382437 0.6214909 cg09844573
5 COX7A2 75953853 0.2056934 0.2195010 0.2449027 0.6214909 cg06809298
31 COX7A2 75954053 0.6797633 0.7130981 0.2507770 0.6214909 cg25716013
8 HLA-DPB1 33048286 0.8099935 0.8510260 0.2673529 0.6349633 cg09234582
10 HLA-DPB1 33048310 0.8032586 0.8410928 0.2981181 0.6797093 cg13349035
55 IFITM1 312518 0.0490676 0.0631639 0.3580291 0.7849100 cg05432003
48 HLA-DPB1 33048529 0.8921467 0.9204202 0.3763096 0.7944315 cg06437840
56 UPK3B 76145673 0.6233565 0.6362010 0.4024983 0.8193716 cg05372444
16 RNF39 30039432 0.4834165 0.5140914 0.4185187 0.8226057 cg13401893
9 HLA-DPB1 33048291 0.8495713 0.8788058 0.4612102 0.8661700 cg25045942
11 RNF39 30039374 0.2369935 0.2837008 0.4710749 0.8661700 cg20249327
50 HLA-DPB1 33048555 0.8798610 0.9063878 0.5083086 0.8721866 cg19990651
4 RNF39 30039175 0.2645229 0.2484897 0.5101264 0.8721866 cg03343571
15 RNF39 30039408 0.2505998 0.2834426 0.5302796 0.8721866 cg07382347
36 GFPT2 179741121 0.6099365 0.5804630 0.5355532 0.8721866 cg02891314
20 RNF39 30039476 0.3121350 0.3567159 0.5829150 0.8743192 cg10930308
39 TLR1 38805732 0.1407696 0.1252848 0.5838557 0.8743192 cg02016764
41 GFPT2 179740915 0.6507088 0.6231930 0.6085513 0.8743192 cg13944838
51 HLA-DPB1 33048558 0.8833427 0.9128768 0.6085841 0.8743192 cg01132696
37 GFPT2 179741105 0.5669895 0.5403248 0.6135573 0.8743192 cg23248424
18 RNF39 30039442 0.5046425 0.5320067 0.6554747 0.9112697 cg10568066
17 RNF39 30039435 0.4208703 0.4520116 0.6785132 0.9208393 cg12633154
12 RNF39 30039376 0.2624746 0.2953810 0.7094274 0.9237632 cg15877520
3 RNF39 30039151 0.1071649 0.1074936 0.7130804 0.9237632 cg18930910
7 SMAD3 67361773 0.5495308 0.5643506 0.7536808 0.9278314 cg24961286
45 HLA-DPB1 33048483 0.8869167 0.9152459 0.7566380 0.9278314 cg03229061
6 COX7A2 75953935 0.0872796 0.0873752 0.7650540 0.9278314 cg19367436
2 RNF39 30039142 0.1191231 0.1084619 0.8291989 0.9620290 cg00947782
46 HLA-DPB1 33048485 0.8542852 0.8782200 0.8463198 0.9620290 cg17588455
25 HOOK2 12877188 0.3100569 0.3262296 0.8594934 0.9620290 cg23899408
21 TTC39C 21572657 0.1164864 0.1077130 0.8670164 0.9620290 cg18719665
57 UPK3B 76145633 0.6969410 0.7009889 0.8776405 0.9620290 cg16453056
40 HOOK2 12877001 0.2608195 0.2961543 0.9123817 0.9812407 cg11738485
22 TTC39C 21572635 0.2504695 0.2470906 0.9656566 0.9880360 cg05401069
23 TTC39C 21572623 0.2459859 0.2419658 0.9656566 0.9880360 cg12639429
14 RNF39 30039403 0.4156483 0.4382731 0.9804417 0.9880360 cg09279736
44 HLA-DPB1 33048469 0.8456642 0.8746810 0.9880360 0.9880360 cg10850215

3.1.1.2 Figure5: The Differential methylated CpGsites between SSc patients and Controls

[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD4+ T cells is 7"
[1] "Plot the figure of EIF2AK2 cg17326313"

[1] "Plot the figure of PARP9 cg00959259"

[1] "Plot the figure of IFI44L cg03607951"

[1] "Plot the figure of IFITM1 cg11694510"

[1] "Plot the figure of PARP9 cg08122652"

[1] "Plot the figure of MX1 cg08924203"

[1] "Plot the figure of HELZ2 cg06064964"

3.1.2 Validation of differential methylated CpGsites between dcSSc patients and Controls

3.1.2.1 Table 8: The Differential methylated CpGsites between dcSSc patients and Controls

Gene Pos Mean.CD4.dc Mean.CD4.NC P.value.CD4.dc.NC FDR Cgname
5 COX7A2 75953853 0.1582780 0.2195010 0.0029650 0.0828283 cg06809298
38 EIF2AK2 37383568 0.1382443 0.1826725 0.0065317 0.0828283 cg17326313
52 IFI44L 79085586 0.6998180 0.7436687 0.0067221 0.0828283 cg03607951
31 COX7A2 75954053 0.6191697 0.7130981 0.0077760 0.0828283 cg25716013
27 PARP9 122281975 0.4618118 0.5290290 0.0078438 0.0828283 cg00959259
49 HLA-DPB1 33048540 0.8485089 0.9221222 0.0087188 0.0828283 cg14870156
50 HLA-DPB1 33048555 0.8322881 0.9063878 0.0202448 0.1511792 cg19990651
8 HLA-DPB1 33048286 0.7585495 0.8510260 0.0221044 0.1511792 cg09234582
10 HLA-DPB1 33048310 0.7549862 0.8410928 0.0284030 0.1511792 cg13349035
47 HLA-DPB1 33048502 0.8621385 0.9422507 0.0290367 0.1511792 cg26645432
43 BRDT 92417998 0.4807120 0.3211686 0.0291749 0.1511792 cg01081438
6 COX7A2 75953935 0.0708456 0.0873752 0.0320718 0.1523412 cg19367436
26 PARP9 122281939 0.7555214 0.7916144 0.0393835 0.1726815 cg08122652
48 HLA-DPB1 33048529 0.8453626 0.9204202 0.0448613 0.1826497 cg06437840
1 MX1 42798747 0.0613389 0.0650165 0.0625835 0.2378174 cg08924203
9 HLA-DPB1 33048291 0.8106489 0.8788058 0.0705215 0.2512328 cg25045942
46 HLA-DPB1 33048485 0.8065949 0.8782200 0.0901437 0.2854550 cg17588455
51 HLA-DPB1 33048558 0.8400719 0.9128768 0.0901437 0.2854550 cg01132696
24 IFITM1 313354 0.2903140 0.3098730 0.1562886 0.4688659 cg11694510
19 RNF39 30039466 0.1980040 0.2484926 0.1673785 0.4770286 cg16078649
34 HELZ2 62199181 0.0485558 0.0373344 0.1926590 0.5135914 cg06064964
54 IFI44L 79085765 0.4823066 0.4984651 0.2048245 0.5135914 cg00855901
30 BRDT 92414782 0.7355643 0.7659456 0.2133566 0.5135914 cg02935097
33 HELZ2 62199156 0.0271085 0.0191877 0.2190334 0.5135914 cg11779113
3 RNF39 30039151 0.0913823 0.1074936 0.2319753 0.5135914 cg18930910
7 SMAD3 67361773 0.6247913 0.5643506 0.2392935 0.5135914 cg24961286
2 RNF39 30039142 0.1024869 0.1084619 0.2505736 0.5135914 cg00947782
56 UPK3B 76145673 0.6251090 0.6362010 0.2522905 0.5135914 cg05372444
4 RNF39 30039175 0.2371108 0.2484897 0.2814859 0.5466522 cg03343571
45 HLA-DPB1 33048483 0.8503734 0.9152459 0.2877117 0.5466522 cg03229061
13 RNF39 30039380 0.2058499 0.2633600 0.3159570 0.5777219 cg13918754
44 HLA-DPB1 33048469 0.8001562 0.8746810 0.3328402 0.5777219 cg10850215
11 RNF39 30039374 0.2305346 0.2837008 0.3435172 0.5777219 cg20249327
22 TTC39C 21572635 0.2332309 0.2470906 0.3446061 0.5777219 cg05401069
42 FAM132A 1178246 0.8489704 0.8213389 0.3926775 0.6208186 cg24345856
18 RNF39 30039442 0.4861955 0.5320067 0.3991158 0.6208186 cg10568066
28 BRDT 92414722 0.3675997 0.3848972 0.4029875 0.6208186 cg14732540
36 GFPT2 179741121 0.6390522 0.5804630 0.4240775 0.6361162 cg02891314
37 GFPT2 179741105 0.5964695 0.5403248 0.4529365 0.6491525 cg23248424
23 TTC39C 21572623 0.2302636 0.2419658 0.4555456 0.6491525 cg12639429
17 RNF39 30039435 0.4065901 0.4520116 0.4794792 0.6665930 cg12633154
20 RNF39 30039476 0.3049676 0.3567159 0.4929225 0.6679323 cg10930308
15 RNF39 30039408 0.2471065 0.2834426 0.5106213 0.6679323 cg07382347
21 TTC39C 21572657 0.1065458 0.1077130 0.5234849 0.6679323 cg18719665
41 GFPT2 179740915 0.6795025 0.6231930 0.5352826 0.6679323 cg13944838
16 RNF39 30039432 0.4732537 0.5140914 0.5469832 0.6679323 cg13401893
29 BRDT 92414737 0.5535320 0.5645251 0.5507512 0.6679323 cg13299824
53 IFI44L 79085713 0.6809374 0.6830388 0.6192145 0.7353172 cg17980508
12 RNF39 30039376 0.2577388 0.2953810 0.6365307 0.7404541 cg15877520
14 RNF39 30039403 0.3974284 0.4382731 0.6663552 0.7573606 cg09279736
55 IFITM1 312518 0.0555557 0.0631639 0.6776384 0.7573606 cg05432003
35 HELZ2 62199190 0.0293048 0.0314240 0.7006219 0.7679894 cg09844573
32 HELZ2 62199034 0.1061342 0.0909342 0.7890495 0.8387980 cg17593958
25 HOOK2 12877188 0.3005064 0.3262296 0.7946507 0.8387980 cg23899408
40 HOOK2 12877001 0.2393487 0.2961543 0.8224753 0.8523835 cg11738485
39 TLR1 38805732 0.1288417 0.1252848 0.9908838 1.0000000 cg02016764
57 UPK3B 76145633 0.6945542 0.7009889 1.0000000 1.0000000 cg16453056

3.1.2.2 Figure6: The Differential methylated CpGsites between dcSSc patients and Controls

[1] "As there are no CpGsite showed significant difference between dcSSc patients and controls, there is no Figure 6 in our analysis."

3.1.3 Validation of differential methylated CpGsites between lcSSc patients and Controls

3.1.3.1 Table 9: The Differential methylated CpGsites between lcSSc patients and Controls

Gene Pos Mean.CD4.lc Mean.CD4.NC P.value.CD4.lc.NC FDR Cgname
38 EIF2AK2 37383568 0.1140921 0.1826725 0.0001064 0.0056791 cg17326313
27 PARP9 122281975 0.4062810 0.5290290 0.0002542 0.0056791 cg00959259
24 IFITM1 313354 0.2443503 0.3098730 0.0002989 0.0056791 cg11694510
52 IFI44L 79085586 0.6557509 0.7436687 0.0004057 0.0057818 cg03607951
34 HELZ2 62199181 0.0761952 0.0373344 0.0026312 0.0285027 cg06064964
26 PARP9 122281939 0.6950776 0.7916144 0.0033381 0.0285027 cg08122652
1 MX1 42798747 0.0544927 0.0650165 0.0035003 0.0285027 cg08924203
42 FAM132A 1178246 0.6711351 0.8213389 0.0176429 0.1130039 cg24345856
32 HELZ2 62199034 0.1436982 0.0909342 0.0178427 0.1130039 cg17593958
54 IFI44L 79085765 0.4376539 0.4984651 0.0348712 0.1987658 cg00855901
30 BRDT 92414782 0.7303421 0.7659456 0.0431068 0.2128604 cg02935097
35 HELZ2 62199190 0.0546971 0.0314240 0.0448127 0.2128604 cg09844573
33 HELZ2 62199156 0.0362710 0.0191877 0.0606307 0.2658423 cg11779113
53 IFI44L 79085713 0.6188783 0.6830388 0.0687262 0.2782739 cg17980508
4 RNF39 30039175 0.2827976 0.2484897 0.0732300 0.2782739 cg03343571
29 BRDT 92414737 0.5381976 0.5645251 0.0994260 0.3542053 cg13299824
43 BRDT 92417998 0.4070290 0.3211686 0.1260836 0.4227508 cg01081438
28 BRDT 92414722 0.3643889 0.3848972 0.1742262 0.5517164 cg14732540
45 HLA-DPB1 33048483 0.9112788 0.9152459 0.2034523 0.6103568 cg03229061
6 COX7A2 75953935 0.0987120 0.0873752 0.2214451 0.6311185 cg19367436
2 RNF39 30039142 0.1302140 0.1084619 0.2336400 0.6341658 cg00947782
13 RNF39 30039380 0.2111889 0.2633600 0.2575123 0.6671909 cg13918754
46 HLA-DPB1 33048485 0.8860788 0.8782200 0.3177340 0.7642193 cg17588455
19 RNF39 30039466 0.2087589 0.2484926 0.3217765 0.7642193 cg16078649
55 IFITM1 312518 0.0458236 0.0631639 0.3364106 0.7670161 cg05432003
39 TLR1 38805732 0.1489023 0.1252848 0.4332000 0.9158092 cg02016764
50 HLA-DPB1 33048555 0.9115762 0.9063878 0.4338044 0.9158092 cg19990651
21 TTC39C 21572657 0.1231134 0.1077130 0.4609924 0.9187244 cg18719665
44 HLA-DPB1 33048469 0.8760028 0.8746810 0.4772753 0.9187244 cg10850215
16 RNF39 30039432 0.4901918 0.5140914 0.4835392 0.9187244 cg13401893
22 TTC39C 21572635 0.2619618 0.2470906 0.5128915 0.9294981 cg05401069
23 TTC39C 21572623 0.2564674 0.2419658 0.5218235 0.9294981 cg12639429
5 COX7A2 75953853 0.2386779 0.2195010 0.5694953 0.9352133 cg06809298
51 HLA-DPB1 33048558 0.9121899 0.9128768 0.5905075 0.9352133 cg01132696
49 HLA-DPB1 33048540 0.9171819 0.9221222 0.6129827 0.9352133 cg14870156
7 SMAD3 67361773 0.4993572 0.5643506 0.6608297 0.9352133 cg24961286
15 RNF39 30039408 0.2529286 0.2834426 0.6918790 0.9352133 cg07382347
3 RNF39 30039151 0.1176867 0.1074936 0.7096815 0.9352133 cg18930910
47 HLA-DPB1 33048502 0.9365151 0.9422507 0.7145440 0.9352133 cg26645432
40 HOOK2 12877001 0.2751334 0.2961543 0.7359427 0.9352133 cg11738485
31 COX7A2 75954053 0.7201590 0.7130981 0.7413143 0.9352133 cg25716013
56 UPK3B 76145673 0.6221882 0.6362010 0.7497569 0.9352133 cg05372444
11 RNF39 30039374 0.2412995 0.2837008 0.7608970 0.9352133 cg20249327
9 HLA-DPB1 33048291 0.8755195 0.8788058 0.7626484 0.9352133 cg25045942
14 RNF39 30039403 0.4277949 0.4382731 0.7716939 0.9352133 cg09279736
36 GFPT2 179741121 0.5905260 0.5804630 0.7841616 0.9352133 cg02891314
20 RNF39 30039476 0.3169132 0.3567159 0.7949805 0.9352133 cg10930308
41 GFPT2 179740915 0.6315130 0.6231930 0.7990228 0.9352133 cg13944838
48 HLA-DPB1 33048529 0.9233361 0.9204202 0.8115257 0.9352133 cg06437840
57 UPK3B 76145633 0.6985323 0.7009889 0.8203625 0.9352133 cg16453056
12 RNF39 30039376 0.2656319 0.2953810 0.8651315 0.9493894 cg15877520
37 GFPT2 179741105 0.5473362 0.5403248 0.8818589 0.9493894 cg23248424
10 HLA-DPB1 33048310 0.8354402 0.8410928 0.8827656 0.9493894 cg13349035
8 HLA-DPB1 33048286 0.8442894 0.8510260 0.9049794 0.9552561 cg09234582
17 RNF39 30039435 0.4303904 0.4520116 0.9607979 0.9787582 cg12633154
25 HOOK2 12877188 0.3164238 0.3262296 0.9615870 0.9787582 cg23899408
18 RNF39 30039442 0.5169406 0.5320067 1.0000000 1.0000000 cg10568066

3.1.3.2 Figure7: The Differential methylated CpGsites between lcSSc patients and Controls

[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD4+ T cells is 7"
[1] "Plot the figure of EIF2AK2 cg17326313"

[1] "Plot the figure of PARP9 cg00959259"

[1] "Plot the figure of IFITM1 cg11694510"

[1] "Plot the figure of IFI44L cg03607951"

[1] "Plot the figure of HELZ2 cg06064964"

[1] "Plot the figure of PARP9 cg08122652"

[1] "Plot the figure of MX1 cg08924203"

3.1.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients

3.1.4.1 Table 10: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

Gene Pos Mean.CD4.dc Mean.CD4.lc P.value.CD4.dc.lc FDR Cgname
5 COX7A2 75953853 0.1582780 0.2386779 0.0071676 0.2096029 cg06809298
50 HLA-DPB1 33048555 0.8322881 0.9115762 0.0122522 0.2096029 cg19990651
31 COX7A2 75954053 0.6191697 0.7201590 0.0156750 0.2096029 cg25716013
6 COX7A2 75953935 0.0708456 0.0987120 0.0172076 0.2096029 cg19367436
24 IFITM1 313354 0.2903140 0.2443503 0.0183862 0.2096029 cg11694510
46 HLA-DPB1 33048485 0.8065949 0.8860788 0.0312288 0.2812870 cg17588455
4 RNF39 30039175 0.2371108 0.2827976 0.0386756 0.2812870 cg03343571
8 HLA-DPB1 33048286 0.7585495 0.8442894 0.0444137 0.2812870 cg09234582
49 HLA-DPB1 33048540 0.8485089 0.9171819 0.0444137 0.2812870 cg14870156
48 HLA-DPB1 33048529 0.8453626 0.9233361 0.0604479 0.2891391 cg06437840
10 HLA-DPB1 33048310 0.7549862 0.8354402 0.0618647 0.2891391 cg13349035
47 HLA-DPB1 33048502 0.8621385 0.9365151 0.0659440 0.2891391 cg26645432
51 HLA-DPB1 33048558 0.8400719 0.9121899 0.0659440 0.2891391 cg01132696
35 HELZ2 62199190 0.0293048 0.0546971 0.0766858 0.3122209 cg09844573
2 RNF39 30039142 0.1024869 0.1302140 0.0844665 0.3195026 cg00947782
9 HLA-DPB1 33048291 0.8106489 0.8755195 0.0896849 0.3195026 cg25045942
42 FAM132A 1178246 0.8489704 0.6711351 0.1264878 0.4241061 cg24345856
38 EIF2AK2 37383568 0.1382443 0.1140921 0.1464178 0.4532251 cg17326313
3 RNF39 30039151 0.0913823 0.1176867 0.1510750 0.4532251 cg18930910
32 HELZ2 62199034 0.1061342 0.1436982 0.1643902 0.4685121 cg17593958
45 HLA-DPB1 33048483 0.8503734 0.9112788 0.1827480 0.4960304 cg03229061
7 SMAD3 67361773 0.6247913 0.4993572 0.2220643 0.5508070 cg24961286
53 IFI44L 79085713 0.6809374 0.6188783 0.2228357 0.5508070 cg17980508
34 HELZ2 62199181 0.0485558 0.0761952 0.2319187 0.5508070 cg06064964
52 IFI44L 79085586 0.6998180 0.6557509 0.2456493 0.5594492 cg03607951
43 BRDT 92417998 0.4807120 0.4070290 0.2551874 0.5594492 cg01081438
22 TTC39C 21572635 0.2332309 0.2619618 0.2790440 0.5858389 cg05401069
44 HLA-DPB1 33048469 0.8001562 0.8760028 0.2877805 0.5858389 cg10850215
27 PARP9 122281975 0.4618118 0.4062810 0.3234273 0.6204948 cg00959259
54 IFI44L 79085765 0.4823066 0.4376539 0.3377640 0.6204948 cg00855901
18 RNF39 30039442 0.4861955 0.5169406 0.3408351 0.6204948 cg10568066
1 MX1 42798747 0.0613389 0.0544927 0.3592338 0.6204948 cg08924203
23 TTC39C 21572623 0.2302636 0.2564674 0.3592338 0.6204948 cg12639429
26 PARP9 122281939 0.7555214 0.6950776 0.3831148 0.6398978 cg08122652
14 RNF39 30039403 0.3974284 0.4277949 0.3997432 0.6398978 cg09279736
21 TTC39C 21572657 0.1065458 0.1231134 0.4041460 0.6398978 cg18719665
29 BRDT 92414737 0.5535320 0.5381976 0.4198151 0.6467422 cg13299824
20 RNF39 30039476 0.3049676 0.3169132 0.4900499 0.7350749 cg10930308
40 HOOK2 12877001 0.2393487 0.2751334 0.5208424 0.7612312 cg11738485
36 GFPT2 179741121 0.6390522 0.5905260 0.5570375 0.7629681 cg02891314
11 RNF39 30039374 0.2305346 0.2412995 0.5714019 0.7629681 cg20249327
17 RNF39 30039435 0.4065901 0.4303904 0.5755724 0.7629681 cg12633154
30 BRDT 92414782 0.7355643 0.7303421 0.5755724 0.7629681 cg02935097
37 GFPT2 179741105 0.5964695 0.5473362 0.6328136 0.7901433 cg23248424
33 HELZ2 62199156 0.0271085 0.0362710 0.6370923 0.7901433 cg11779113
55 IFITM1 312518 0.0555557 0.0458236 0.6376595 0.7901433 cg05432003
39 TLR1 38805732 0.1288417 0.1489023 0.6648621 0.7982768 cg02016764
15 RNF39 30039408 0.2471065 0.2529286 0.6722331 0.7982768 cg07382347
19 RNF39 30039466 0.1980040 0.2087589 0.7093540 0.8123098 cg16078649
41 GFPT2 179740915 0.6795025 0.6315130 0.7125525 0.8123098 cg13944838
12 RNF39 30039376 0.2577388 0.2656319 0.7536718 0.8329511 cg15877520
16 RNF39 30039432 0.4732537 0.4901918 0.7718955 0.8329511 cg13401893
13 RNF39 30039380 0.2058499 0.2111889 0.7744984 0.8329511 cg13918754
28 BRDT 92414722 0.3675997 0.3643889 0.8166164 0.8619840 cg14732540
25 HOOK2 12877188 0.3005064 0.3164238 0.8807380 0.9127649 cg23899408
56 UPK3B 76145673 0.6251090 0.6221882 0.9011242 0.9172157 cg05372444
57 UPK3B 76145633 0.6945542 0.6985323 0.9891186 0.9891186 cg16453056

3.1.4.2 Figure8: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 8 in our analysis."

3.2 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD8+

3.2.1 Validation of differential methylated CpGsites between SSc patients and Controls

3.2.1.1 Table 11: The Differential methylated CpGsites between SSc patients and Controls

Gene Pos Mean.CD8.SSc Mean.CD8.NC P.value.CD8.SSC.NC FDR Cgname
27 PARP9 122281975 0.4531487 0.5968228 0.0000000 0.0000002 cg00959259
26 PARP9 122281939 0.7320359 0.8323341 0.0000001 0.0000020 cg08122652
38 EIF2AK2 37383568 0.1373269 0.1882193 0.0000971 0.0018443 cg17326313
34 HELZ2 62199181 0.0451481 0.0214664 0.0002035 0.0028996 cg06064964
21 TTC39C 21572657 0.1848003 0.1419552 0.0003293 0.0037542 cg18719665
54 IFI44L 79085765 0.5151405 0.6067145 0.0011990 0.0113905 cg00855901
22 TTC39C 21572635 0.3820672 0.3329965 0.0054331 0.0442407 cg05401069
32 HELZ2 62199034 0.1427749 0.0981128 0.0069887 0.0451370 cg17593958
33 HELZ2 62199156 0.0221550 0.0106671 0.0071269 0.0451370 cg11779113
35 HELZ2 62199190 0.0334972 0.0185647 0.0096154 0.0545651 cg09844573
23 TTC39C 21572623 0.3587072 0.3148537 0.0105301 0.0545651 cg12639429
53 IFI44L 79085713 0.6866851 0.7410939 0.0116753 0.0554579 cg17980508
20 RNF39 30039476 0.3051805 0.3870814 0.0160688 0.0704556 cg10930308
52 IFI44L 79085586 0.7097750 0.7625005 0.0178789 0.0727926 cg03607951
14 RNF39 30039403 0.4364698 0.5066883 0.0214113 0.0810791 cg09279736
11 RNF39 30039374 0.2453951 0.3210745 0.0227590 0.0810791 cg20249327
19 RNF39 30039466 0.2398981 0.3018692 0.0269289 0.0902911 cg16078649
17 RNF39 30039435 0.4457716 0.5147477 0.0368050 0.1165493 cg12633154
16 RNF39 30039432 0.4890092 0.5487349 0.0445974 0.1337921 cg13401893
12 RNF39 30039376 0.2472879 0.3088533 0.0508454 0.1410246 cg15877520
15 RNF39 30039408 0.2767715 0.3401470 0.0519564 0.1410246 cg07382347
49 HLA-DPB1 33048540 0.8985396 0.9300191 0.0613516 0.1589565 cg14870156
18 RNF39 30039442 0.5566290 0.6089304 0.0861232 0.2109022 cg10568066
51 HLA-DPB1 33048558 0.8842849 0.9185070 0.0915257 0.2109022 cg01132696
45 HLA-DPB1 33048483 0.9146446 0.9459825 0.0925010 0.2109022 cg03229061
1 MX1 42798747 0.0694463 0.0772312 0.1102259 0.2416490 cg08924203
42 FAM132A 1178246 0.7041153 0.7990064 0.1274810 0.2656621 cg24345856
13 RNF39 30039380 0.2259111 0.2931618 0.1305007 0.2656621 cg13918754
8 HLA-DPB1 33048286 0.8528574 0.8854463 0.1394408 0.2735732 cg09234582
24 IFITM1 313354 0.2657604 0.2781218 0.1439859 0.2735732 cg11694510
47 HLA-DPB1 33048502 0.9263918 0.9495350 0.1624473 0.2986934 cg26645432
10 HLA-DPB1 33048310 0.8406343 0.8746341 0.1713249 0.3051725 cg13349035
9 HLA-DPB1 33048291 0.8783046 0.9075440 0.1830702 0.3162122 cg25045942
43 BRDT 92417998 0.4293984 0.3385588 0.2222715 0.3726315 cg01081438
46 HLA-DPB1 33048485 0.8838146 0.9019680 0.2389443 0.3891379 cg17588455
39 TLR1 38805732 0.2242038 0.1519158 0.2815084 0.4457217 cg02016764
50 HLA-DPB1 33048555 0.9042304 0.9244570 0.4691117 0.7065182 cg19990651
41 GFPT2 179740915 0.6326464 0.6066592 0.4710121 0.7065182 cg13944838
37 GFPT2 179741105 0.5720316 0.5438813 0.5151081 0.7458898 cg23248424
55 IFITM1 312518 0.0591742 0.0645218 0.5326765 0.7458898 cg05432003
31 COX7A2 75954053 0.6679577 0.6796820 0.5392675 0.7458898 cg25716013
36 GFPT2 179741121 0.6222384 0.5961929 0.5496030 0.7458898 cg02891314
40 HOOK2 12877001 0.2531282 0.2778928 0.6561935 0.8698379 cg11738485
48 HLA-DPB1 33048529 0.8988812 0.9228805 0.6946645 0.8845146 cg06437840
6 COX7A2 75953935 0.1161680 0.1196888 0.6983010 0.8845146 cg19367436
4 RNF39 30039175 0.3684328 0.3765410 0.7489301 0.9244078 cg03343571
30 BRDT 92414782 0.5152659 0.5015247 0.7843399 0.9244078 cg02935097
5 COX7A2 75953853 0.2208525 0.2254708 0.8146425 0.9244078 cg06809298
44 HLA-DPB1 33048469 0.8432144 0.8622766 0.8185363 0.9244078 cg10850215
7 SMAD3 67361773 0.5528822 0.5717843 0.8556844 0.9244078 cg24961286
3 RNF39 30039151 0.1535606 0.1491135 0.8600892 0.9244078 cg18930910
56 UPK3B 76145673 0.6460271 0.6409087 0.8600892 0.9244078 cg05372444
2 RNF39 30039142 0.1907816 0.1891776 0.8820034 0.9244078 cg00947782
57 UPK3B 76145633 0.6982444 0.6990565 0.9076810 0.9244078 cg16453056
28 BRDT 92414722 0.3303334 0.3304857 0.9076835 0.9244078 cg14732540
29 BRDT 92414737 0.4273772 0.4210830 0.9081902 0.9244078 cg13299824
25 HOOK2 12877188 0.3265455 0.3373459 0.9716002 0.9716002 cg23899408

3.2.1.2 Figure9 : The Differential methylated CpGsites between SSc patients and Controls

[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD8+ T cells is 9"
[1] "Plot the figure of PARP9 cg00959259"

[1] "Plot the figure of PARP9 cg08122652"

[1] "Plot the figure of EIF2AK2 cg17326313"

[1] "Plot the figure of HELZ2 cg06064964"

[1] "Plot the figure of TTC39C cg18719665"

[1] "Plot the figure of IFI44L cg00855901"

[1] "Plot the figure of TTC39C cg05401069"

[1] "Plot the figure of HELZ2 cg17593958"

[1] "Plot the figure of HELZ2 cg11779113"

3.2.2 Validation of differential methylated CpGsites between dcSSc patients and Controls

3.2.2.1 Table 12: The Differential methylated CpGsites between dcSSc patients and Controls

Gene Pos Mean.CD8.dc Mean.CD8.NC P.value.CD8.dc.NC FDR Cgname
27 PARP9 122281975 0.5038614 0.5968228 0.0000795 0.0045336 cg00959259
26 PARP9 122281939 0.7752162 0.8323341 0.0004673 0.0133193 cg08122652
34 HELZ2 62199181 0.0403199 0.0214664 0.0017552 0.0333493 cg06064964
21 TTC39C 21572657 0.1751158 0.1419552 0.0051675 0.0736364 cg18719665
22 TTC39C 21572635 0.3737943 0.3329965 0.0200640 0.1460961 cg05401069
9 HLA-DPB1 33048291 0.8440094 0.9075440 0.0203633 0.1460961 cg25045942
10 HLA-DPB1 33048310 0.8029228 0.8746341 0.0203633 0.1460961 cg13349035
38 EIF2AK2 37383568 0.1523055 0.1882193 0.0205047 0.1460961 cg17326313
8 HLA-DPB1 33048286 0.8158911 0.8854463 0.0328369 0.2079672 cg09234582
50 HLA-DPB1 33048555 0.8772847 0.9244570 0.0460668 0.2625807 cg19990651
23 TTC39C 21572623 0.3483870 0.3148537 0.0508476 0.2634830 cg12639429
51 HLA-DPB1 33048558 0.8637292 0.9185070 0.0602995 0.2864225 cg01132696
31 COX7A2 75954053 0.6152673 0.6796820 0.0738199 0.3236717 cg25716013
20 RNF39 30039476 0.3027517 0.3870814 0.0800138 0.3257705 cg10930308
47 HLA-DPB1 33048502 0.9052612 0.9495350 0.0933254 0.3384623 cg26645432
6 COX7A2 75953935 0.0983593 0.1196888 0.0985566 0.3384623 cg19367436
54 IFI44L 79085765 0.5381196 0.6067145 0.1010910 0.3384623 cg00855901
5 COX7A2 75953853 0.1791361 0.2254708 0.1152786 0.3384623 cg06809298
12 RNF39 30039376 0.2454873 0.3088533 0.1166722 0.3384623 cg15877520
33 HELZ2 62199156 0.0183079 0.0106671 0.1187587 0.3384623 cg11779113
49 HLA-DPB1 33048540 0.8913260 0.9300191 0.1367150 0.3710835 cg14870156
14 RNF39 30039403 0.4428490 0.5066883 0.1455487 0.3722053 cg09279736
11 RNF39 30039374 0.2511929 0.3210745 0.1613889 0.3722053 cg20249327
7 SMAD3 67361773 0.6526138 0.5717843 0.1662787 0.3722053 cg24961286
32 HELZ2 62199034 0.1303204 0.0981128 0.1700332 0.3722053 cg17593958
36 GFPT2 179741121 0.6758027 0.5961929 0.1766241 0.3722053 cg02891314
17 RNF39 30039435 0.4492864 0.5147477 0.1784679 0.3722053 cg12633154
18 RNF39 30039442 0.5503101 0.6089304 0.1844433 0.3722053 cg10568066
35 HELZ2 62199190 0.0282865 0.0185647 0.1893676 0.3722053 cg09844573
37 GFPT2 179741105 0.6153956 0.5438813 0.2097935 0.3986077 cg23248424
41 GFPT2 179740915 0.6764403 0.6066592 0.2263120 0.4161220 cg13944838
19 RNF39 30039466 0.2486829 0.3018692 0.2494308 0.4442987 cg16078649
16 RNF39 30039432 0.5015302 0.5487349 0.2969993 0.5129987 cg13401893
46 HLA-DPB1 33048485 0.8731776 0.9019680 0.3109870 0.5213605 cg17588455
15 RNF39 30039408 0.2907931 0.3401470 0.3229185 0.5254711 cg07382347
56 UPK3B 76145673 0.6591430 0.6409087 0.3318765 0.5254711 cg05372444
52 IFI44L 79085586 0.7342337 0.7625005 0.3439880 0.5293755 cg03607951
13 RNF39 30039380 0.2266518 0.2931618 0.3597039 0.5293755 cg13918754
39 TLR1 38805732 0.2455374 0.1519158 0.3622043 0.5293755 cg02016764
45 HLA-DPB1 33048483 0.9137198 0.9459825 0.4044165 0.5705369 cg03229061
53 IFI44L 79085713 0.7196792 0.7410939 0.4103862 0.5705369 cg17980508
43 BRDT 92417998 0.4218728 0.3385588 0.5459604 0.7409462 cg01081438
57 UPK3B 76145633 0.6889555 0.6990565 0.5677746 0.7526314 cg16453056
42 FAM132A 1178246 0.7904919 0.7990064 0.5837457 0.7551444 cg24345856
2 RNF39 30039142 0.1778969 0.1891776 0.5961666 0.7551444 cg00947782
48 HLA-DPB1 33048529 0.8844981 0.9228805 0.6348471 0.7866584 cg06437840
3 RNF39 30039151 0.1489598 0.1491135 0.7786131 0.9116599 cg18930910
55 IFITM1 312518 0.0638008 0.0645218 0.7807075 0.9116599 cg05432003
28 BRDT 92414722 0.3375056 0.3304857 0.7925551 0.9116599 cg14732540
25 HOOK2 12877188 0.3175145 0.3373459 0.7997017 0.9116599 cg23899408
44 HLA-DPB1 33048469 0.8301764 0.8622766 0.8163607 0.9124032 cg10850215
4 RNF39 30039175 0.3676492 0.3765410 0.8347777 0.9150448 cg03343571
30 BRDT 92414782 0.5136856 0.5015247 0.8646147 0.9219336 cg02935097
29 BRDT 92414737 0.4350134 0.4210830 0.8787515 0.9219336 cg13299824
1 MX1 42798747 0.0767360 0.0772312 0.8951382 0.9219336 cg08924203
40 HOOK2 12877001 0.2404004 0.2778928 0.9057593 0.9219336 cg11738485
24 IFITM1 313354 0.2827623 0.2781218 0.9785245 0.9785245 cg11694510

3.2.2.2 Figure10 : The Differential methylated CpGsites between dcSSc patients and Controls

[1] "The number of significant differential methylated CpGsites between dcSSc patients and normal controls in CD8+ T cells is 3"
[1] "Plot the figure of PARP9 cg00959259"

[1] "Plot the figure of PARP9 cg08122652"

[1] "Plot the figure of HELZ2 cg06064964"

3.2.3 Validation of differential methylated CpGsites between lcSSc patients and Controls

3.2.3.1 Table 13: The Differential methylated CpGsites between lcSSc patients and Controls

Gene Pos Mean.CD8.lc Mean.CD8.NC P.value.CD8.lc.NC FDR Cgname
27 PARP9 122281975 0.4227211 0.5968228 0.0000000 0.0000023 cg00959259
26 PARP9 122281939 0.7061277 0.8323341 0.0000004 0.0000123 cg08122652
38 EIF2AK2 37383568 0.1283398 0.1882193 0.0001445 0.0027447 cg17326313
54 IFI44L 79085765 0.5013530 0.6067145 0.0007354 0.0104792 cg00855901
21 TTC39C 21572657 0.1911325 0.1419552 0.0023798 0.0249457 cg18719665
34 HELZ2 62199181 0.0482206 0.0214664 0.0030540 0.0249457 cg06064964
53 IFI44L 79085713 0.6668886 0.7410939 0.0030635 0.0249457 cg17980508
32 HELZ2 62199034 0.1507004 0.0981128 0.0049158 0.0350251 cg17593958
35 HELZ2 62199190 0.0368130 0.0185647 0.0067862 0.0424276 cg09844573
33 HELZ2 62199156 0.0246032 0.0106671 0.0074434 0.0424276 cg11779113
52 IFI44L 79085586 0.6950998 0.7625005 0.0082411 0.0427037 cg03607951
1 MX1 42798747 0.0649603 0.0772312 0.0174810 0.0830349 cg08924203
19 RNF39 30039466 0.2344922 0.3018692 0.0220196 0.0955158 cg16078649
22 TTC39C 21572635 0.3874764 0.3329965 0.0257309 0.0955158 cg05401069
11 RNF39 30039374 0.2418272 0.3210745 0.0281741 0.0955158 cg20249327
14 RNF39 30039403 0.4325441 0.5066883 0.0284098 0.0955158 cg09279736
23 TTC39C 21572623 0.3654550 0.3148537 0.0284872 0.0955158 cg12639429
20 RNF39 30039476 0.3066752 0.3870814 0.0329618 0.1043789 cg10930308
24 IFITM1 313354 0.2552977 0.2781218 0.0363332 0.1069390 cg11694510
16 RNF39 30039432 0.4813039 0.5487349 0.0375225 0.1069390 cg13401893
15 RNF39 30039408 0.2681428 0.3401470 0.0426072 0.1156480 cg07382347
17 RNF39 30039435 0.4436087 0.5147477 0.0492870 0.1276981 cg12633154
42 FAM132A 1178246 0.6509604 0.7990064 0.0797333 0.1922498 cg24345856
45 HLA-DPB1 33048483 0.9151426 0.9459825 0.0809473 0.1922498 cg03229061
12 RNF39 30039376 0.2483960 0.3088533 0.1050740 0.2395688 cg15877520
49 HLA-DPB1 33048540 0.9024238 0.9300191 0.1162624 0.2548830 cg14870156
13 RNF39 30039380 0.2254552 0.2931618 0.1416151 0.2955955 cg13918754
18 RNF39 30039442 0.5605175 0.6089304 0.1452048 0.2955955 cg10568066
43 BRDT 92417998 0.4340296 0.3385588 0.2019771 0.3969894 cg01081438
51 HLA-DPB1 33048558 0.8953533 0.9185070 0.2886716 0.5484760 cg01132696
46 HLA-DPB1 33048485 0.8895422 0.9019680 0.3495811 0.6427782 cg17588455
47 HLA-DPB1 33048502 0.9377699 0.9495350 0.4261264 0.7287358 cg26645432
5 COX7A2 75953853 0.2458823 0.2254708 0.4329821 0.7287358 cg06809298
39 TLR1 38805732 0.1967748 0.1519158 0.4346845 0.7287358 cg02016764
55 IFITM1 312518 0.0545476 0.0645218 0.4846278 0.7892510 cg05432003
7 SMAD3 67361773 0.4988609 0.5717843 0.5013891 0.7938662 cg24961286
6 COX7A2 75953935 0.1268532 0.1196888 0.5333464 0.8216418 cg19367436
8 HLA-DPB1 33048286 0.8756058 0.8854463 0.5869590 0.8578632 cg09234582
40 HOOK2 12877001 0.2614503 0.2778928 0.5869590 0.8578632 cg11738485
44 HLA-DPB1 33048469 0.8502348 0.8622766 0.6349855 0.9048543 cg10850215
56 UPK3B 76145673 0.6379558 0.6409087 0.6554565 0.9112444 cg05372444
31 COX7A2 75954053 0.7003826 0.6796820 0.6814189 0.9247828 cg25716013
50 HLA-DPB1 33048555 0.9187396 0.9244570 0.7481197 0.9687679 cg19990651
4 RNF39 30039175 0.3689150 0.3765410 0.7693881 0.9687679 cg03343571
10 HLA-DPB1 33048310 0.8638414 0.8746341 0.7934026 0.9687679 cg13349035
30 BRDT 92414782 0.5162384 0.5015247 0.7980256 0.9687679 cg02935097
57 UPK3B 76145633 0.7039606 0.6990565 0.8081719 0.9687679 cg16453056
48 HLA-DPB1 33048529 0.9066260 0.9228805 0.8286788 0.9687679 cg06437840
9 HLA-DPB1 33048291 0.8994094 0.9075440 0.8330581 0.9687679 cg25045942
2 RNF39 30039142 0.1987107 0.1891776 0.8645366 0.9687679 cg00947782
25 HOOK2 12877188 0.3324504 0.3373459 0.8933038 0.9687679 cg23899408
41 GFPT2 179740915 0.6056963 0.6066592 0.8933038 0.9687679 cg13944838
36 GFPT2 179741121 0.5892757 0.5961929 0.9007842 0.9687679 cg02891314
29 BRDT 92414737 0.4226780 0.4210830 0.9636324 0.9948029 cg13299824
3 RNF39 30039151 0.1563919 0.1491135 0.9685953 0.9948029 cg18930910
28 BRDT 92414722 0.3259197 0.3304857 0.9842946 0.9948029 cg14732540
37 GFPT2 179741105 0.5453461 0.5438813 0.9948029 0.9948029 cg23248424

3.2.3.2 Figure11: The Differential methylated CpGsites between lcSSc patients and Controls

[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD8+ T cells is 11"
[1] "Plot the figure of PARP9 cg00959259"

[1] "Plot the figure of PARP9 cg08122652"

[1] "Plot the figure of EIF2AK2 cg17326313"

[1] "Plot the figure of IFI44L cg00855901"

[1] "Plot the figure of TTC39C cg18719665"

[1] "Plot the figure of HELZ2 cg06064964"

[1] "Plot the figure of IFI44L cg17980508"

[1] "Plot the figure of HELZ2 cg17593958"

[1] "Plot the figure of HELZ2 cg09844573"

[1] "Plot the figure of HELZ2 cg11779113"

[1] "Plot the figure of IFI44L cg03607951"

3.2.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients

3.2.4.1 Table 14: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

Gene Pos Mean.CD8.dc Mean.CD8.lc P.value.CD8.dc.lc FDR Cgname
5 COX7A2 75953853 0.1791361 0.2458823 0.0403777 0.4625642 cg06809298
6 COX7A2 75953935 0.0983593 0.1268532 0.0403777 0.4625642 cg19367436
26 PARP9 122281939 0.7752162 0.7061277 0.0496820 0.4625642 cg08122652
9 HLA-DPB1 33048291 0.8440094 0.8994094 0.0497442 0.4625642 cg25045942
50 HLA-DPB1 33048555 0.8772847 0.9187396 0.0503863 0.4625642 cg19990651
31 COX7A2 75954053 0.6152673 0.7003826 0.0529465 0.4625642 cg25716013
27 PARP9 122281975 0.5038614 0.4227211 0.0568061 0.4625642 cg00959259
1 MX1 42798747 0.0767360 0.0649603 0.0803430 0.5204622 cg08924203
8 HLA-DPB1 33048286 0.8158911 0.8756058 0.0899516 0.5204622 cg09234582
7 SMAD3 67361773 0.6526138 0.4988609 0.0917468 0.5204622 cg24961286
10 HLA-DPB1 33048310 0.8029228 0.8638414 0.1004401 0.5204622 cg13349035
24 IFITM1 313354 0.2827623 0.2552977 0.1242443 0.5901604 cg11694510
53 IFI44L 79085713 0.7196792 0.6668886 0.1559242 0.6836677 cg17980508
52 IFI44L 79085586 0.7342337 0.6950998 0.1915700 0.7340673 cg03607951
36 GFPT2 179741121 0.6758027 0.5892757 0.1931756 0.7340673 cg02891314
47 HLA-DPB1 33048502 0.9052612 0.9377699 0.2120866 0.7555585 cg26645432
42 FAM132A 1178246 0.7904919 0.6509604 0.2313265 0.7756242 cg24345856
37 GFPT2 179741105 0.6153956 0.5453461 0.2522421 0.7987666 cg23248424
35 HELZ2 62199190 0.0282865 0.0368130 0.2769422 0.8150000 cg09844573
41 GFPT2 179740915 0.6764403 0.6056963 0.2859649 0.8150000 cg13944838
15 RNF39 30039408 0.2907931 0.2681428 0.3225341 0.8571533 cg07382347
38 EIF2AK2 37383568 0.1523055 0.1283398 0.3464354 0.8571533 cg17326313
56 UPK3B 76145673 0.6591430 0.6379558 0.3484969 0.8571533 cg05372444
54 IFI44L 79085765 0.5381196 0.5013530 0.3609066 0.8571533 cg00855901
51 HLA-DPB1 33048558 0.8637292 0.8953533 0.3870911 0.8825678 cg01132696
32 HELZ2 62199034 0.1303204 0.1507004 0.4171925 0.9146142 cg17593958
2 RNF39 30039142 0.1778969 0.1987107 0.4525638 0.9297820 cg00947782
55 IFITM1 312518 0.0638008 0.0545476 0.5255517 0.9297820 cg05432003
19 RNF39 30039466 0.2486829 0.2344922 0.5513504 0.9297820 cg16078649
39 TLR1 38805732 0.2455374 0.1967748 0.6064685 0.9297820 cg02016764
25 HOOK2 12877188 0.3175145 0.3324504 0.6142730 0.9297820 cg23899408
16 RNF39 30039432 0.5015302 0.4813039 0.6173306 0.9297820 cg13401893
43 BRDT 92417998 0.4218728 0.4340296 0.6173306 0.9297820 cg01081438
45 HLA-DPB1 33048483 0.9137198 0.9151426 0.6196804 0.9297820 cg03229061
57 UPK3B 76145633 0.6889555 0.7039606 0.6226125 0.9297820 cg16453056
12 RNF39 30039376 0.2454873 0.2483960 0.6355221 0.9297820 cg15877520
23 TTC39C 21572623 0.3483870 0.3654550 0.6493002 0.9297820 cg12639429
14 RNF39 30039403 0.4428490 0.4325441 0.6539311 0.9297820 cg09279736
33 HELZ2 62199156 0.0183079 0.0246032 0.6596025 0.9297820 cg11779113
46 HLA-DPB1 33048485 0.8731776 0.8895422 0.6705576 0.9297820 cg17588455
21 TTC39C 21572657 0.1751158 0.1911325 0.6851025 0.9297820 cg18719665
40 HOOK2 12877001 0.2404004 0.2614503 0.6851025 0.9297820 cg11738485
11 RNF39 30039374 0.2511929 0.2418272 0.7103662 0.9318861 cg20249327
44 HLA-DPB1 33048469 0.8301764 0.8502348 0.7443168 0.9318861 cg10850215
22 TTC39C 21572635 0.3737943 0.3874764 0.7587485 0.9318861 cg05401069
13 RNF39 30039380 0.2266518 0.2254552 0.7658032 0.9318861 cg13918754
17 RNF39 30039435 0.4492864 0.4436087 0.7683973 0.9318861 cg12633154
49 HLA-DPB1 33048540 0.8913260 0.9024238 0.7902422 0.9368355 cg14870156
48 HLA-DPB1 33048529 0.8844981 0.9066260 0.8118948 0.9368355 cg06437840
4 RNF39 30039175 0.3676492 0.3689150 0.8459705 0.9368355 cg03343571
28 BRDT 92414722 0.3375056 0.3259197 0.8477344 0.9368355 cg14732540
20 RNF39 30039476 0.3027517 0.3066752 0.8678401 0.9368355 cg10930308
34 HELZ2 62199181 0.0403199 0.0482206 0.8710926 0.9368355 cg06064964
29 BRDT 92414737 0.4350134 0.4226780 0.8880295 0.9373645 cg13299824
30 BRDT 92414782 0.5136856 0.5162384 0.9586838 0.9897883 cg02935097
3 RNF39 30039151 0.1489598 0.1563919 0.9897883 0.9897883 cg18930910
18 RNF39 30039442 0.5503101 0.5605175 0.9897883 0.9897883 cg10568066

3.2.4.2 Figure12: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 12 in our analysis."

3.3 Validation of differential methylated CpGsites only in the validation stage due to the sequencing advantage in CD4+

3.3.1 Validation of differential methylated CpGsites between SSc patients and Controls

3.3.1.1 Table 14: The Differential methylated CpGsites between SSc patients and Controls

Gene Pos Mean.CD4.SSc Mean.CD4.NC P.value.CD4.SSC.NC FDR
51 IFITM1 313408 0.1955548 0.2401521 0.0000949 0.0146091
11 MX1 42798829 0.1168171 0.1497797 0.0011679 0.0899277
128 FAM132A 1178105 0.9777073 0.9809027 0.0025672 0.0921532
76 EIF2AK2 37383588 0.0711415 0.0929983 0.0025984 0.0921532
14 MX1 42798857 0.1503967 0.1895065 0.0029920 0.0921532
15 MX1 42798863 0.1674460 0.2113965 0.0042052 0.1079333
5 MX1 42798749 0.0286869 0.0338268 0.0054003 0.1188066
122 FAM132A 1178182 0.7938068 0.8086350 0.0068399 0.1206740
123 FAM132A 1178172 0.8643950 0.8761917 0.0070524 0.1206740
1 MX1 42798695 0.0338730 0.0390410 0.0082350 0.1268184
9 MX1 42798816 0.1304322 0.1608932 0.0099131 0.1371737
2 MX1 42798698 0.0282268 0.0316677 0.0106889 0.1371737
13 MX1 42798847 0.1282379 0.1568913 0.0119716 0.1418178
80 EIF2AK2 37383730 0.0253558 0.0313496 0.0163700 0.1664561
12 MX1 42798837 0.0746994 0.0905090 0.0171172 0.1664561
78 EIF2AK2 37383679 0.0158425 0.0179496 0.0172941 0.1664561
4 MX1 42798733 0.0331928 0.0377474 0.0206115 0.1867161
7 MX1 42798781 0.0654812 0.0746964 0.0309712 0.2572960
10 MX1 42798818 0.0810102 0.0970545 0.0317443 0.2572960
34 SMAD3 67361798 0.9060494 0.8799748 0.0362919 0.2794477
6 MX1 42798765 0.0289796 0.0330338 0.0413520 0.3032482
3 MX1 42798723 0.0486544 0.0540432 0.0487092 0.3399600
151 UPK3B 76145628 0.7230687 0.7463902 0.0507732 0.3399600
8 MX1 42798813 0.1292800 0.1508762 0.0610138 0.3846584
27 RNF39 30039239 0.3312149 0.3015051 0.0624445 0.3846584
120 FAM132A 1178202 0.7812274 0.7903459 0.0702747 0.4162423
60 BRDT 92414661 0.5202705 0.5484402 0.0871049 0.4968208
124 FAM132A 1178162 0.8109639 0.8198598 0.1048672 0.5767696
63 BRDT 92414770 0.7353634 0.7569150 0.1373808 0.7148964
119 FAM132A 1178207 0.8465924 0.8540344 0.1522422 0.7148964
30 COX7A2 75953883 0.1743206 0.1921192 0.1530608 0.7148964
61 BRDT 92414719 0.3010934 0.3236102 0.1572996 0.7148964
24 RNF39 30039208 0.1624442 0.1495977 0.1661652 0.7148964
68 HELZ2 62199061 0.0411729 0.0312027 0.1669424 0.7148964
62 BRDT 92414751 0.7196543 0.7433972 0.1722787 0.7148964
130 BRDT 92418017 0.9711326 0.9729621 0.1742732 0.7148964
47 RNF39 30039364 0.1061779 0.0955109 0.1785568 0.7148964
64 BRDT 92414793 0.8163762 0.8339878 0.1807333 0.7148964
150 UPK3B 76145689 0.3547661 0.3694151 0.1810452 0.7148964
56 HOOK2 12877215 0.2840337 0.3121684 0.1901034 0.7237129
145 IFITM1 312434 0.1630115 0.1794032 0.1926768 0.7237129
20 RNF39 30039158 0.1156256 0.1093117 0.2076499 0.7613831
58 HOOK2 12877276 0.2752086 0.3066603 0.2175675 0.7650575
94 HOOK2 12876911 0.2828709 0.3201762 0.2248536 0.7650575
50 RNF39 30039418 0.4570728 0.4976985 0.2258832 0.7650575
33 COX7A2 75953974 0.2202770 0.2413041 0.2287168 0.7650575
59 BRDT 92414650 0.3998200 0.4164258 0.2334916 0.7650575
77 EIF2AK2 37383623 0.0138249 0.0167856 0.2412769 0.7740969
153 UPK3B 76145606 0.3855753 0.3740667 0.2747625 0.8217816
146 IFITM1 312463 0.1262688 0.1426939 0.2784136 0.8217816
57 HOOK2 12877235 0.3330295 0.3619532 0.2806918 0.8217816
148 UPK3B 76145702 0.2904265 0.3040766 0.3009317 0.8217816
29 COX7A2 75953829 0.1618291 0.1724741 0.3224437 0.8217816
35 SMAD3 67361821 0.8945688 0.8890964 0.3291888 0.8217816
121 FAM132A 1178192 0.9283847 0.9309795 0.3360343 0.8217816
42 RNF39 30039307 0.1850312 0.2300563 0.3440129 0.8217816
79 EIF2AK2 37383713 0.0101216 0.0106117 0.3459727 0.8217816
55 HOOK2 12877201 0.3077689 0.3345829 0.3550682 0.8217816
65 COX7A2 75954022 0.5263550 0.5549263 0.3612235 0.8217816
28 COX7A2 75953821 0.0619963 0.0654486 0.3638846 0.8217816
32 COX7A2 75953960 0.1931812 0.2027426 0.3645119 0.8217816
88 HOOK2 12876946 0.2456540 0.2807895 0.3754273 0.8217816
17 RNF39 30039127 0.3283798 0.3144216 0.3768842 0.8217816
37 HLA-DPB1 33048370 0.6899866 0.7210373 0.3801472 0.8217816
149 UPK3B 76145693 0.5299942 0.5369975 0.3864734 0.8217816
41 RNF39 30039303 0.1976302 0.2418742 0.3875510 0.8217816
125 FAM132A 1178150 0.9169066 0.9182135 0.3963196 0.8217816
154 UPK3B 76145589 0.1747223 0.1647508 0.4106594 0.8217816
93 HOOK2 12876918 0.2633712 0.2971163 0.4237725 0.8217816
143 IFI44L 79085647 0.1163383 0.1218025 0.4240147 0.8217816
22 RNF39 30039202 0.1638384 0.1512972 0.4241843 0.8217816
67 COX7A2 75954122 0.4190122 0.4398731 0.4320049 0.8217816
99 GFPT2 179740970 0.5587564 0.5300324 0.4406541 0.8217816
100 GFPT2 179740963 0.6233814 0.5924331 0.4521171 0.8217816
75 GFPT2 179741039 0.5830682 0.5537992 0.4671794 0.8217816
71 GFPT2 179741067 0.5383177 0.5113622 0.4731907 0.8217816
95 GFPT2 179741008 0.5286138 0.5032499 0.4755354 0.8217816
16 RNF39 30039123 0.3791472 0.3629646 0.4801742 0.8217816
49 RNF39 30039415 0.2359129 0.2553079 0.4853385 0.8217816
69 GFPT2 179741101 0.5746154 0.5434945 0.4976512 0.8217816
73 GFPT2 179741060 0.5947270 0.5650352 0.5038686 0.8217816
89 HOOK2 12876944 0.2477893 0.2838409 0.5057098 0.8217816
98 GFPT2 179740992 0.6001045 0.5708047 0.5057098 0.8217816
45 RNF39 30039349 0.2009290 0.2340406 0.5080327 0.8217816
44 RNF39 30039323 0.2805337 0.3194670 0.5080353 0.8217816
97 GFPT2 179740994 0.6138890 0.5845215 0.5368514 0.8217816
107 GFPT2 179740906 0.6369850 0.6065319 0.5368514 0.8217816
40 RNF39 30039278 0.3558052 0.3843611 0.5399645 0.8217816
70 GFPT2 179741081 0.5646860 0.5399389 0.5420071 0.8217816
96 GFPT2 179740999 0.5939736 0.5663734 0.5431922 0.8217816
102 GFPT2 179740955 0.6409681 0.6124159 0.5431922 0.8217816
104 GFPT2 179740935 0.6459324 0.6171712 0.5431922 0.8217816
137 HLA-DPB1 33048549 0.8968477 0.9253918 0.5473711 0.8217816
101 GFPT2 179740957 0.6386792 0.6101367 0.5624329 0.8217816
105 GFPT2 179740920 0.5982046 0.5698056 0.5624329 0.8217816
66 COX7A2 75954118 0.4623212 0.4781793 0.5628955 0.8217816
74 GFPT2 179741042 0.4431661 0.4191338 0.5681999 0.8217816
126 FAM132A 1178136 0.9709623 0.9725677 0.5681999 0.8217816
87 HOOK2 12876948 0.2486727 0.2842421 0.5689180 0.8217816
36 SMAD3 67361896 0.8394041 0.8322659 0.5695113 0.8217816
83 HOOK2 12876997 0.2241197 0.2582667 0.5754383 0.8217816
108 GFPT2 179740900 0.5975451 0.5676209 0.5754383 0.8217816
127 FAM132A 1178118 0.9508636 0.9528701 0.5762065 0.8217816
133 HLA-DPB1 33048433 0.8975962 0.9242818 0.5790187 0.8217816
92 HOOK2 12876926 0.2523331 0.2876337 0.5819932 0.8217816
103 GFPT2 179740940 0.6012562 0.5719450 0.5819932 0.8217816
141 HLA-DPB1 33048592 0.9197516 0.9436297 0.5824403 0.8217816
86 HOOK2 12876969 0.2424377 0.2782543 0.5885823 0.8217816
152 UPK3B 76145620 0.8057483 0.8004547 0.5899746 0.8217816
31 COX7A2 75953937 0.1017073 0.1035921 0.5946883 0.8217816
43 RNF39 30039313 0.2146751 0.2466175 0.5998517 0.8217816
129 FAM132A 1178086 0.9187048 0.9190379 0.5998517 0.8217816
117 GFPT2 179740825 0.7377502 0.7123661 0.6085513 0.8217816
23 RNF39 30039206 0.1358605 0.1264953 0.6101158 0.8217816
135 HLA-DPB1 33048542 0.0583057 0.0588600 0.6136680 0.8217816
114 GFPT2 179740852 0.6996409 0.6786374 0.6220274 0.8257949
109 GFPT2 179740888 0.5905199 0.5590831 0.6356299 0.8352430
110 GFPT2 179740869 0.6988038 0.6738677 0.6493550 0.8352430
139 HLA-DPB1 33048575 0.9134333 0.9383515 0.6509926 0.8352430
54 HOOK2 12877138 0.2702749 0.2930451 0.6562624 0.8352430
106 GFPT2 179740918 0.6198811 0.5948481 0.6562624 0.8352430
38 RNF39 30039271 0.1960425 0.2340739 0.6713819 0.8447493
115 GFPT2 179740840 0.7194545 0.6979930 0.6771574 0.8447493
53 HOOK2 12877107 0.2480657 0.2701639 0.6841783 0.8447493
72 GFPT2 179741063 0.5387418 0.5144854 0.6856731 0.8447493
113 GFPT2 179740855 0.7409110 0.7204086 0.6912264 0.8448323
147 UPK3B 76145717 0.4342985 0.4410031 0.7110318 0.8556371
112 GFPT2 179740861 0.7174508 0.6963664 0.7125277 0.8556371
25 RNF39 30039232 0.1983630 0.1933329 0.7167350 0.8556371
84 HOOK2 12876993 0.2338669 0.2672557 0.7268540 0.8610424
90 HOOK2 12876942 0.2502241 0.2861320 0.7557871 0.8790559
91 HOOK2 12876937 0.2422273 0.2769211 0.7630755 0.8790559
116 GFPT2 179740832 0.7361678 0.7171415 0.7630755 0.8790559
81 TLR1 38805839 0.0536032 0.0543074 0.7648928 0.8790559
52 HOOK2 12877099 0.2461531 0.2670255 0.7777140 0.8871700
111 GFPT2 179740867 0.6858757 0.6670694 0.7850629 0.8889683
21 RNF39 30039186 0.1412413 0.1364882 0.7987598 0.8925497
82 HOOK2 12877020 0.2328244 0.2684078 0.7998172 0.8925497
39 RNF39 30039274 0.2159565 0.2529471 0.8111903 0.8987288
142 HLA-DPB1 33048602 0.5428538 0.5777344 0.8181502 0.8999652
46 RNF39 30039354 0.2312497 0.2679622 0.8330229 0.9094062
132 HLA-DPB1 33048423 0.9086892 0.9338485 0.8385433 0.9094062
134 HLA-DPB1 33048444 0.8681408 0.8946963 0.8541111 0.9198119
118 GFPT2 179740822 0.7016392 0.6859685 0.8670164 0.9272259
144 IFITM1 312419 0.0662380 0.0582821 0.9342208 0.9798859
85 HOOK2 12876987 0.2393534 0.2738826 0.9351801 0.9798859
136 HLA-DPB1 33048544 0.9186744 0.9400067 0.9402342 0.9798859
19 RNF39 30039132 0.0991727 0.1029618 0.9417085 0.9798859
48 RNF39 30039411 0.4280441 0.4423376 0.9569891 0.9891029
140 HLA-DPB1 33048581 0.9028995 0.9264820 0.9681035 0.9920238
18 RNF39 30039130 0.1580897 0.1545091 0.9765315 0.9920238
26 RNF39 30039235 0.1493717 0.1443090 0.9843528 0.9920238
131 HLA-DPB1 33048417 0.8914680 0.9188951 0.9881057 0.9920238
138 HLA-DPB1 33048571 0.9124444 0.9370998 0.9920238 0.9920238

3.3.1.2 Figure12: The Differential methylated CpGsites between SSc patients and Controls

[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD4+ T cells is 1"
[1] "Plot the figure of IFITM1 313408"

3.3.2 Validation of differential methylated CpGsites between dcSSc patients and Controls

3.3.2.1 Table 15: The Differential methylated CpGsites between dcSSc patients and Controls

Gene Pos Mean.CD4.dc Mean.CD4.NC P.value.CD4.dc.NC FDR
28 COX7A2 75953821 0.0446434 0.0654486 0.0014698 0.1859804
30 COX7A2 75953883 0.1399584 0.1921192 0.0024153 0.1859804
151 UPK3B 76145628 0.7062744 0.7463902 0.0045330 0.2326928
65 COX7A2 75954022 0.4518312 0.5549263 0.0065018 0.2503208
29 COX7A2 75953829 0.1264856 0.1724741 0.0082136 0.2529792
123 FAM132A 1178172 0.8628519 0.8761917 0.0103875 0.2666113
32 COX7A2 75953960 0.1555675 0.2027426 0.0188227 0.3651751
31 COX7A2 75953937 0.0805141 0.1035921 0.0213414 0.3651751
33 COX7A2 75953974 0.1823139 0.2413041 0.0213414 0.3651751
122 FAM132A 1178182 0.7929911 0.8086350 0.0244646 0.3767549
66 COX7A2 75954118 0.4110438 0.4781793 0.0298290 0.4018708
67 COX7A2 75954122 0.3666147 0.4398731 0.0313146 0.4018708
76 EIF2AK2 37383588 0.0759636 0.0929983 0.0340806 0.4037239
78 EIF2AK2 37383679 0.0143214 0.0179496 0.0393835 0.4332186
37 HLA-DPB1 33048370 0.6273491 0.7210373 0.0737282 0.7037514
139 HLA-DPB1 33048575 0.8728620 0.9383515 0.0763787 0.7037514
51 IFITM1 313408 0.2193774 0.2401521 0.0865762 0.7037514
34 SMAD3 67361798 0.9058747 0.8799748 0.0953294 0.7037514
128 FAM132A 1178105 0.9789670 0.9809027 0.0972014 0.7037514
80 EIF2AK2 37383730 0.0263226 0.0313496 0.1109068 0.7037514
4 MX1 42798733 0.0346634 0.0377474 0.1262778 0.7037514
136 HLA-DPB1 33048544 0.8773159 0.9400067 0.1272663 0.7037514
133 HLA-DPB1 33048433 0.8554437 0.9242818 0.1433082 0.7037514
11 MX1 42798829 0.1365556 0.1497797 0.1559733 0.7037514
135 HLA-DPB1 33048542 0.0683155 0.0588600 0.1581536 0.7037514
94 HOOK2 12876911 0.2628716 0.3201762 0.1669421 0.7037514
21 RNF39 30039186 0.1254795 0.1364882 0.1702702 0.7037514
14 MX1 42798857 0.1718197 0.1895065 0.1708868 0.7037514
58 HOOK2 12877276 0.2590516 0.3066603 0.1784679 0.7037514
5 MX1 42798749 0.0309253 0.0338268 0.1905622 0.7037514
138 HLA-DPB1 33048571 0.8724026 0.9370998 0.2077564 0.7037514
42 RNF39 30039307 0.1733708 0.2300563 0.2178187 0.7037514
50 RNF39 30039418 0.4442470 0.4976985 0.2248090 0.7037514
142 HLA-DPB1 33048602 0.4494760 0.5777344 0.2253595 0.7037514
148 UPK3B 76145702 0.2841578 0.3040766 0.2348383 0.7037514
15 MX1 42798863 0.1933493 0.2113965 0.2448278 0.7037514
137 HLA-DPB1 33048549 0.8561483 0.9253918 0.2468203 0.7037514
79 EIF2AK2 37383713 0.0083365 0.0106117 0.2480905 0.7037514
18 RNF39 30039130 0.1422862 0.1545091 0.2505736 0.7037514
27 RNF39 30039239 0.3243063 0.3015051 0.2544149 0.7037514
120 FAM132A 1178202 0.7827009 0.7903459 0.2652243 0.7037514
56 HOOK2 12877215 0.2709562 0.3121684 0.2676775 0.7037514
13 MX1 42798847 0.1465303 0.1568913 0.2756029 0.7037514
19 RNF39 30039132 0.0922963 0.1029618 0.2898598 0.7037514
57 HOOK2 12877235 0.3206069 0.3619532 0.2919194 0.7037514
124 FAM132A 1178162 0.8130103 0.8198598 0.3070953 0.7037514
119 FAM132A 1178207 0.8479868 0.8540344 0.3080908 0.7037514
54 HOOK2 12877138 0.2542766 0.2930451 0.3088587 0.7037514
117 GFPT2 179740825 0.7798747 0.7123661 0.3088587 0.7037514
141 HLA-DPB1 33048592 0.8785906 0.9436297 0.3199569 0.7037514
44 RNF39 30039323 0.2670671 0.3194670 0.3214626 0.7037514
60 BRDT 92414661 0.5263980 0.5484402 0.3249814 0.7037514
144 IFITM1 312419 0.0729589 0.0582821 0.3383131 0.7037514
25 RNF39 30039232 0.1782205 0.1933329 0.3435172 0.7037514
75 GFPT2 179741039 0.6135393 0.5537992 0.3435172 0.7037514
55 HOOK2 12877201 0.2941553 0.3345829 0.3446061 0.7037514
92 HOOK2 12876926 0.2325951 0.2876337 0.3446061 0.7037514
131 HLA-DPB1 33048417 0.8528855 0.9188951 0.3520793 0.7037514
150 UPK3B 76145689 0.3570678 0.3694151 0.3539311 0.7037514
52 HOOK2 12877099 0.2306115 0.2670255 0.3634106 0.7037514
132 HLA-DPB1 33048423 0.8696502 0.9338485 0.3719926 0.7037514
49 RNF39 30039415 0.2266577 0.2553079 0.3725329 0.7037514
93 HOOK2 12876918 0.2439106 0.2971163 0.3730440 0.7037514
114 GFPT2 179740852 0.7368690 0.6786374 0.3730440 0.7037514
26 RNF39 30039235 0.1358569 0.1443090 0.3787070 0.7037514
126 FAM132A 1178136 0.9701882 0.9725677 0.3825257 0.7037514
2 MX1 42798698 0.0308387 0.0316677 0.3828306 0.7037514
100 GFPT2 179740963 0.6543772 0.5924331 0.3828306 0.7037514
74 GFPT2 179741042 0.4692564 0.4191338 0.3926775 0.7037514
104 GFPT2 179740935 0.6806278 0.6171712 0.3927697 0.7037514
88 HOOK2 12876946 0.2254400 0.2807895 0.4028602 0.7037514
113 GFPT2 179740855 0.7807848 0.7204086 0.4028602 0.7037514
36 SMAD3 67361896 0.8435264 0.8322659 0.4042664 0.7037514
3 MX1 42798723 0.0513214 0.0540432 0.4131011 0.7037514
12 MX1 42798837 0.0850276 0.0905090 0.4131011 0.7037514
110 GFPT2 179740869 0.7353703 0.6738677 0.4131011 0.7037514
41 RNF39 30039303 0.1915649 0.2418742 0.4134546 0.7037514
71 GFPT2 179741067 0.5638664 0.5113622 0.4134546 0.7037514
121 FAM132A 1178192 0.9283732 0.9309795 0.4134546 0.7037514
134 HLA-DPB1 33048444 0.8251486 0.8946963 0.4138171 0.7037514
98 GFPT2 179740992 0.6312012 0.5708047 0.4234915 0.7037514
99 GFPT2 179740970 0.5854953 0.5300324 0.4234915 0.7037514
109 GFPT2 179740888 0.6252246 0.5590831 0.4234915 0.7037514
115 GFPT2 179740840 0.7598012 0.6979930 0.4234915 0.7037514
116 GFPT2 179740832 0.7763586 0.7171415 0.4234915 0.7037514
140 HLA-DPB1 33048581 0.8656858 0.9264820 0.4262430 0.7037514
102 GFPT2 179740955 0.6733490 0.6124159 0.4340299 0.7037514
112 GFPT2 179740861 0.7560015 0.6963664 0.4340299 0.7037514
53 HOOK2 12877107 0.2337943 0.2701639 0.4447151 0.7037514
101 GFPT2 179740957 0.6711285 0.6101367 0.4447151 0.7037514
118 GFPT2 179740822 0.7419350 0.6859685 0.4447151 0.7037514
77 EIF2AK2 37383623 0.0132245 0.0167856 0.4481670 0.7037514
125 FAM132A 1178150 0.9220973 0.9182135 0.4529283 0.7037514
40 RNF39 30039278 0.3409712 0.3843611 0.4529365 0.7037514
73 GFPT2 179741060 0.6235241 0.5650352 0.4568674 0.7037514
23 RNF39 30039206 0.1187244 0.1264953 0.4641705 0.7037514
96 GFPT2 179740999 0.6234426 0.5663734 0.4665199 0.7037514
97 GFPT2 179740994 0.6448891 0.5845215 0.4665199 0.7037514
69 GFPT2 179741101 0.5996110 0.5434945 0.4680993 0.7037514
127 FAM132A 1178118 0.9495490 0.9528701 0.4698451 0.7037514
91 HOOK2 12876937 0.2229114 0.2769211 0.4776362 0.7037514
95 GFPT2 179741008 0.5565324 0.5032499 0.4888928 0.7037514
61 BRDT 92414719 0.3078300 0.3236102 0.4910052 0.7037514
45 RNF39 30039349 0.1943104 0.2340406 0.4987776 0.7037514
9 MX1 42798816 0.1525878 0.1608932 0.5002878 0.7037514
87 HOOK2 12876948 0.2287765 0.2842421 0.5002878 0.7037514
103 GFPT2 179740940 0.6335832 0.5719450 0.5002878 0.7037514
105 GFPT2 179740920 0.6286866 0.5698056 0.5002878 0.7037514
107 GFPT2 179740906 0.6711654 0.6065319 0.5002878 0.7037514
43 RNF39 30039313 0.2053626 0.2466175 0.5106213 0.7037514
89 HOOK2 12876944 0.2283631 0.2838409 0.5118192 0.7037514
108 GFPT2 179740900 0.6263760 0.5676209 0.5118192 0.7037514
7 MX1 42798781 0.0723267 0.0746964 0.5234849 0.7134219
47 RNF39 30039364 0.1044725 0.0955109 0.5385277 0.7149419
70 GFPT2 179741081 0.5870507 0.5399389 0.5385277 0.7149419
72 GFPT2 179741063 0.5645206 0.5144854 0.5385277 0.7149419
1 MX1 42798695 0.0381601 0.0390410 0.5472100 0.7202593
82 HOOK2 12877020 0.2123525 0.2684078 0.5592647 0.7219432
38 RNF39 30039271 0.1879945 0.2340739 0.5631068 0.7219432
6 MX1 42798765 0.0317686 0.0330338 0.5714442 0.7219432
106 GFPT2 179740918 0.6526585 0.5948481 0.5714442 0.7219432
129 FAM132A 1178086 0.9193654 0.9190379 0.5719290 0.7219432
111 GFPT2 179740867 0.7217714 0.6670694 0.5837457 0.7305105
62 BRDT 92414751 0.7326712 0.7433972 0.5882033 0.7305105
10 MX1 42798818 0.0941620 0.0970545 0.6087041 0.7439717
130 BRDT 92418017 0.9728535 0.9729621 0.6087041 0.7439717
153 UPK3B 76145606 0.3782685 0.3740667 0.6307751 0.7579801
90 HOOK2 12876942 0.2300281 0.2861320 0.6341167 0.7579801
22 RNF39 30039202 0.1501742 0.1512972 0.6365307 0.7579801
17 RNF39 30039127 0.3078670 0.3144216 0.6398533 0.7579801
83 HOOK2 12876997 0.2060073 0.2582667 0.6599588 0.7621717
147 UPK3B 76145717 0.4323066 0.4410031 0.6599588 0.7621717
149 UPK3B 76145693 0.5311877 0.5369975 0.6599588 0.7621717
35 SMAD3 67361821 0.8864407 0.8890964 0.6631884 0.7621717
143 IFI44L 79085647 0.1195439 0.1218025 0.6709270 0.7628837
68 HELZ2 62199061 0.0356405 0.0312027 0.6751122 0.7628837
81 TLR1 38805839 0.0596818 0.0543074 0.6786693 0.7628837
86 HOOK2 12876969 0.2234150 0.2782543 0.6862044 0.7657643
154 UPK3B 76145589 0.1720512 0.1647508 0.7167959 0.7926289
16 RNF39 30039123 0.3614561 0.3629646 0.7205717 0.7926289
146 IFITM1 312463 0.1562166 0.1426939 0.7498587 0.8189946
63 BRDT 92414770 0.7509697 0.7569150 0.7597665 0.8235646
152 UPK3B 76145620 0.7966523 0.8004547 0.7647386 0.8235646
39 RNF39 30039274 0.2086611 0.2529471 0.7761999 0.8301027
46 RNF39 30039354 0.2246827 0.2679622 0.8044616 0.8528366
8 MX1 42798813 0.1528304 0.1508762 0.8085334 0.8528366
85 HOOK2 12876987 0.2186697 0.2738826 0.8505202 0.8910212
84 HOOK2 12876993 0.2152394 0.2672557 0.8787515 0.9143766
48 RNF39 30039411 0.4167763 0.4423376 0.8894606 0.9193083
59 BRDT 92414650 0.4258523 0.4164258 0.9335398 0.9571429
20 RNF39 30039158 0.1019108 0.1093117 0.9482851 0.9571429
24 RNF39 30039208 0.1471008 0.1495977 0.9488318 0.9571429
145 IFITM1 312434 0.2057482 0.1794032 0.9509277 0.9571429
64 BRDT 92414793 0.8320961 0.8339878 0.9634393 0.9634393

3.3.2.2 Figure13: The Differential methylated CpGsites between dcSSc patients and Controls

[1] "As there are no CpGsite showed significant difference between dcSSc patients and controls, there is no Figure 13 in our analysis."

3.3.3 Validation of differential methylated CpGsites between lcSSc patients and Controls

3.3.3.1 Table 16: The Differential methylated CpGsites between dcSSc lcSSc patients and Controls

Gene Pos Mean.CD4.lc Mean.CD4.NC P.value.CD4.lc.NC FDR
51 IFITM1 313408 0.1796731 0.2401521 0.0000122 0.0018800
11 MX1 42798829 0.1036581 0.1497797 0.0003040 0.0234114
1 MX1 42798695 0.0310149 0.0390410 0.0007168 0.0365720
15 MX1 42798863 0.1501772 0.2113965 0.0011647 0.0365720
14 MX1 42798857 0.1361146 0.1895065 0.0012631 0.0365720
9 MX1 42798816 0.1156618 0.1608932 0.0014249 0.0365720
128 FAM132A 1178105 0.9768675 0.9809027 0.0017163 0.0377596
2 MX1 42798698 0.0264856 0.0316677 0.0024984 0.0448923
5 MX1 42798749 0.0271947 0.0338268 0.0026236 0.0448923
8 MX1 42798813 0.1135797 0.1508762 0.0033381 0.0514067
12 MX1 42798837 0.0678139 0.0905090 0.0048474 0.0678641
13 MX1 42798847 0.1160429 0.1568913 0.0053089 0.0681307
10 MX1 42798818 0.0722424 0.0970545 0.0066373 0.0786262
76 EIF2AK2 37383588 0.0681276 0.0929983 0.0072459 0.0797054
7 MX1 42798781 0.0609176 0.0746964 0.0086127 0.0884234
6 MX1 42798765 0.0271204 0.0330338 0.0125539 0.1208314
3 MX1 42798723 0.0468764 0.0540432 0.0271852 0.2325843
80 EIF2AK2 37383730 0.0247515 0.0313496 0.0271852 0.2325843
122 FAM132A 1178182 0.7943505 0.8086350 0.0301499 0.2419470
4 MX1 42798733 0.0322124 0.0377474 0.0314217 0.2419470
145 IFITM1 312434 0.1337707 0.1794032 0.0478549 0.3509361
24 RNF39 30039208 0.1726732 0.1495977 0.0511500 0.3580500
123 FAM132A 1178172 0.8654238 0.8761917 0.0546959 0.3623529
63 BRDT 92414770 0.7249593 0.7569150 0.0569540 0.3623529
64 BRDT 92414793 0.8058962 0.8339878 0.0588235 0.3623529
146 IFITM1 312463 0.1053054 0.1426939 0.0639694 0.3757275
78 EIF2AK2 37383679 0.0167932 0.0179496 0.0658743 0.3757275
27 RNF39 30039239 0.3358206 0.3015051 0.0700346 0.3767049
125 FAM132A 1178150 0.9134462 0.9182135 0.0711358 0.3767049
59 BRDT 92414650 0.3824652 0.4164258 0.0733841 0.3767049
20 RNF39 30039158 0.1247689 0.1093117 0.0780478 0.3811890
120 FAM132A 1178202 0.7802450 0.7903459 0.0804279 0.3811890
34 SMAD3 67361798 0.9061659 0.8799748 0.0816833 0.3811890
60 BRDT 92414661 0.5161855 0.5484402 0.0881805 0.3994056
68 HELZ2 62199061 0.0448612 0.0312027 0.0951017 0.4184473
17 RNF39 30039127 0.3420550 0.3144216 0.0994260 0.4253225
141 HLA-DPB1 33048592 0.9471922 0.9436297 0.1185622 0.4688546
130 BRDT 92418017 0.9699854 0.9729621 0.1192884 0.4688546
62 BRDT 92414751 0.7109765 0.7433972 0.1217804 0.4688546
124 FAM132A 1178162 0.8095996 0.8198598 0.1217804 0.4688546
22 RNF39 30039202 0.1729478 0.1512972 0.1281305 0.4812707
61 BRDT 92414719 0.2966023 0.3236102 0.1324693 0.4857207
47 RNF39 30039364 0.1073149 0.0955109 0.1438587 0.5152149
23 RNF39 30039206 0.1472846 0.1264953 0.1928652 0.6600457
16 RNF39 30039123 0.3909412 0.3629646 0.1928705 0.6600457
119 FAM132A 1178207 0.8456628 0.8540344 0.2018483 0.6757531
25 RNF39 30039232 0.2117913 0.1933329 0.2077654 0.6807633
150 UPK3B 76145689 0.3532317 0.3694151 0.2276299 0.7238409
153 UPK3B 76145606 0.3904465 0.3740667 0.2303130 0.7238409
77 EIF2AK2 37383623 0.0142002 0.0167856 0.2763252 0.8346787
28 COX7A2 75953821 0.0740679 0.0654486 0.2764196 0.8346787
35 SMAD3 67361821 0.8999875 0.8890964 0.2851982 0.8446256
136 HLA-DPB1 33048544 0.9462467 0.9400067 0.2947441 0.8564262
56 HOOK2 12877215 0.2927520 0.3121684 0.3039772 0.8648714
152 UPK3B 76145620 0.8118123 0.8004547 0.3113647 0.8648714
31 COX7A2 75953937 0.1164504 0.1035921 0.3177720 0.8648714
132 HLA-DPB1 33048423 0.9347152 0.9338485 0.3247835 0.8648714
138 HLA-DPB1 33048571 0.9391389 0.9370998 0.3257308 0.8648714
149 UPK3B 76145693 0.5291985 0.5369975 0.3673767 0.9429335
154 UPK3B 76145589 0.1765031 0.1647508 0.3673767 0.9429335
144 IFITM1 312419 0.0619931 0.0582821 0.4059303 0.9946184
18 RNF39 30039130 0.1686253 0.1545091 0.4105201 0.9946184
143 IFI44L 79085647 0.1143348 0.1218025 0.4157401 0.9946184
50 RNF39 30039418 0.4656233 0.4976985 0.4185943 0.9946184
66 COX7A2 75954118 0.4965062 0.4781793 0.4198065 0.9946184
81 TLR1 38805839 0.0494588 0.0543074 0.4418207 1.0000000
121 FAM132A 1178192 0.9283924 0.9309795 0.4517972 1.0000000
57 HOOK2 12877235 0.3413112 0.3619532 0.4609924 1.0000000
58 HOOK2 12877276 0.2859800 0.3066603 0.4609924 1.0000000
65 COX7A2 75954022 0.5760375 0.5549263 0.4776318 1.0000000
26 RNF39 30039235 0.1583816 0.1443090 0.4791272 1.0000000
19 RNF39 30039132 0.1037569 0.1029618 0.4864167 1.0000000
94 HOOK2 12876911 0.2962037 0.3201762 0.4952656 1.0000000
131 HLA-DPB1 33048417 0.9171898 0.9188951 0.4952986 1.0000000
139 HLA-DPB1 33048575 0.9404808 0.9383515 0.4952986 1.0000000
21 RNF39 30039186 0.1517492 0.1364882 0.5042415 1.0000000
140 HLA-DPB1 33048581 0.9277086 0.9264820 0.5044426 1.0000000
151 UPK3B 76145628 0.7342650 0.7463902 0.5235259 1.0000000
88 HOOK2 12876946 0.2591300 0.2807895 0.5308336 1.0000000
41 RNF39 30039303 0.2016737 0.2418742 0.5408827 1.0000000
55 HOOK2 12877201 0.3168446 0.3345829 0.5490840 1.0000000
29 COX7A2 75953829 0.1864159 0.1724741 0.5594925 1.0000000
142 HLA-DPB1 33048602 0.6051056 0.5777344 0.5610910 1.0000000
148 UPK3B 76145702 0.2946057 0.3040766 0.5649388 1.0000000
32 COX7A2 75953960 0.2193472 0.2027426 0.6103232 1.0000000
95 GFPT2 179741008 0.5100013 0.5032499 0.6249850 1.0000000
99 GFPT2 179740970 0.5409305 0.5300324 0.6249850 1.0000000
67 COX7A2 75954122 0.4539439 0.4398731 0.6278239 1.0000000
79 EIF2AK2 37383713 0.0112373 0.0106117 0.6347781 1.0000000
83 HOOK2 12876997 0.2361947 0.2582667 0.6446345 1.0000000
86 HOOK2 12876969 0.2551195 0.2782543 0.6446345 1.0000000
93 HOOK2 12876918 0.2763449 0.2971163 0.6446345 1.0000000
89 HOOK2 12876944 0.2607402 0.2838409 0.6545528 1.0000000
45 RNF39 30039349 0.2053414 0.2340406 0.6659660 1.0000000
42 RNF39 30039307 0.1928048 0.2300563 0.6762892 1.0000000
69 GFPT2 179741101 0.5579517 0.5434945 0.6785338 1.0000000
100 GFPT2 179740963 0.6027175 0.5924331 0.6846640 1.0000000
70 GFPT2 179741081 0.5497762 0.5399389 0.6888596 1.0000000
71 GFPT2 179741067 0.5212852 0.5113622 0.6888596 1.0000000
73 GFPT2 179741060 0.5755289 0.5650352 0.6992427 1.0000000
84 HOOK2 12876993 0.2462851 0.2672557 0.7050196 1.0000000
107 GFPT2 179740906 0.6141981 0.6065319 0.7152770 1.0000000
134 HLA-DPB1 33048444 0.8968022 0.8946963 0.7252828 1.0000000
135 HLA-DPB1 33048542 0.0516326 0.0588600 0.7341313 1.0000000
98 GFPT2 179740992 0.5793734 0.5708047 0.7359427 1.0000000
118 GFPT2 179740822 0.6747754 0.6859685 0.7359427 1.0000000
97 GFPT2 179740994 0.5932223 0.5845215 0.7463476 1.0000000
129 FAM132A 1178086 0.9182644 0.9190379 0.7501385 1.0000000
49 RNF39 30039415 0.2420830 0.2553079 0.7519581 1.0000000
75 GFPT2 179741039 0.5627541 0.5537992 0.7519581 1.0000000
133 HLA-DPB1 33048433 0.9256979 0.9242818 0.7560148 1.0000000
96 GFPT2 179740999 0.5743277 0.5663734 0.7567983 1.0000000
105 GFPT2 179740920 0.5778832 0.5698056 0.7567983 1.0000000
40 RNF39 30039278 0.3656945 0.3843611 0.7608970 1.0000000
87 HOOK2 12876948 0.2619367 0.2842421 0.7672930 1.0000000
108 GFPT2 179740900 0.5783244 0.5676209 0.7672930 1.0000000
52 HOOK2 12877099 0.2565141 0.2670255 0.7778298 1.0000000
85 HOOK2 12876987 0.2531426 0.2738826 0.7884070 1.0000000
102 GFPT2 179740955 0.6193809 0.6124159 0.7884070 1.0000000
103 GFPT2 179740940 0.5797049 0.5719450 0.7884070 1.0000000
43 RNF39 30039313 0.2208833 0.2466175 0.8043754 1.0000000
127 FAM132A 1178118 0.9517401 0.9528701 0.8058384 1.0000000
101 GFPT2 179740957 0.6170463 0.6101367 0.8096752 1.0000000
30 COX7A2 75953883 0.1982248 0.1921192 0.8190017 1.0000000
104 GFPT2 179740935 0.6228022 0.6171712 0.8310828 1.0000000
106 GFPT2 179740918 0.5980296 0.5948481 0.8418341 1.0000000
44 RNF39 30039323 0.2895114 0.3194670 0.8484676 1.0000000
48 RNF39 30039411 0.4355559 0.4423376 0.8484676 1.0000000
147 UPK3B 76145717 0.4356264 0.4410031 0.8514916 1.0000000
36 SMAD3 67361896 0.8366558 0.8322659 0.8595659 1.0000000
116 GFPT2 179740832 0.7093739 0.7171415 0.8634221 1.0000000
38 RNF39 30039271 0.2014079 0.2340739 0.8716915 1.0000000
74 GFPT2 179741042 0.4257726 0.4191338 0.8716915 1.0000000
126 FAM132A 1178136 0.9714783 0.9725677 0.8827656 1.0000000
54 HOOK2 12877138 0.2809405 0.2930451 0.8959883 1.0000000
39 RNF39 30039274 0.2208201 0.2529471 0.9049794 1.0000000
46 RNF39 30039354 0.2356277 0.2679622 0.9154616 1.0000000
72 GFPT2 179741063 0.5215559 0.5144854 0.9161150 1.0000000
91 HOOK2 12876937 0.2551046 0.2769211 0.9177988 1.0000000
37 HLA-DPB1 33048370 0.7317450 0.7210373 0.9266991 1.0000000
82 HOOK2 12877020 0.2464723 0.2684078 0.9396705 1.0000000
90 HOOK2 12876942 0.2636881 0.2861320 0.9396705 1.0000000
92 HOOK2 12876926 0.2654917 0.2876337 0.9506242 1.0000000
109 GFPT2 179740888 0.5673834 0.5590831 0.9506242 1.0000000
112 GFPT2 179740861 0.6917503 0.6963664 0.9506242 1.0000000
113 GFPT2 179740855 0.7143285 0.7204086 0.9506242 1.0000000
117 GFPT2 179740825 0.7096671 0.7123661 0.9725570 1.0000000
33 COX7A2 75953974 0.2466861 0.2413041 0.9823349 1.0000000
110 GFPT2 179740869 0.6744261 0.6738677 0.9835322 1.0000000
111 GFPT2 179740867 0.6619451 0.6670694 0.9835322 1.0000000
114 GFPT2 179740852 0.6748221 0.6786374 0.9835322 1.0000000
137 HLA-DPB1 33048549 0.9239807 0.9253918 0.9942798 1.0000000
115 GFPT2 179740840 0.6925568 0.6979930 0.9945104 1.0000000
53 HOOK2 12877107 0.2575799 0.2701639 1.0000000 1.0000000

3.3.3.2 Figure14: The Differential methylated CpGsites between dcSSc lcSSc patients and Controls

[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD4+ T cells is 9"
[1] "Plot the figure of IFITM1 313408"

[1] "Plot the figure of MX1 42798829"

[1] "Plot the figure of MX1 42798695"

[1] "Plot the figure of MX1 42798863"

[1] "Plot the figure of MX1 42798857"

[1] "Plot the figure of MX1 42798816"

[1] "Plot the figure of FAM132A 1178105"

[1] "Plot the figure of MX1 42798698"

[1] "Plot the figure of MX1 42798749"

3.3.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients

3.3.4.1 Table 17: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

Gene Pos Mean.CD4.dc Mean.CD4.lc P.value.CD4.dc.lc FDR
28 COX7A2 75953821 0.0446434 0.0740679 0.0012448 0.1916966
65 COX7A2 75954022 0.4518312 0.5760375 0.0031203 0.2402595
51 IFITM1 313408 0.2193774 0.1796731 0.0060829 0.2782194
8 MX1 42798813 0.1528304 0.1135797 0.0122522 0.2782194
30 COX7A2 75953883 0.1399584 0.1982248 0.0122754 0.2782194
31 COX7A2 75953937 0.0805141 0.1164504 0.0133774 0.2782194
32 COX7A2 75953960 0.1555675 0.2193472 0.0133774 0.2782194
1 MX1 42798695 0.0381601 0.0310149 0.0144530 0.2782194
125 FAM132A 1178150 0.9220973 0.9134462 0.0183862 0.2835113
66 COX7A2 75954118 0.4110438 0.4965062 0.0198853 0.2835113
29 COX7A2 75953829 0.1264856 0.1864159 0.0202508 0.2835113
9 MX1 42798816 0.1525878 0.1156618 0.0290299 0.3725503
67 COX7A2 75954122 0.3666147 0.4539439 0.0335651 0.3837527
11 MX1 42798829 0.1365556 0.1036581 0.0360453 0.3837527
33 COX7A2 75953974 0.1823139 0.2466861 0.0373785 0.3837527
10 MX1 42798818 0.0941620 0.0722424 0.0475350 0.4326570
12 MX1 42798837 0.0850276 0.0678139 0.0579914 0.4326570
14 MX1 42798857 0.1718197 0.1361146 0.0579914 0.4326570
15 MX1 42798863 0.1933493 0.1501772 0.0618647 0.4326570
21 RNF39 30039186 0.1254795 0.1517492 0.0659440 0.4326570
136 HLA-DPB1 33048544 0.8773159 0.9462467 0.0659440 0.4326570
2 MX1 42798698 0.0308387 0.0264856 0.0702365 0.4326570
6 MX1 42798765 0.0317686 0.0271204 0.0702365 0.4326570
37 HLA-DPB1 33048370 0.6273491 0.7317450 0.0702365 0.4326570
135 HLA-DPB1 33048542 0.0683155 0.0516326 0.0702365 0.4326570
7 MX1 42798781 0.0723267 0.0609176 0.0794904 0.4708280
25 RNF39 30039232 0.1782205 0.2117913 0.0844242 0.4815304
139 HLA-DPB1 33048575 0.8728620 0.9404808 0.0896849 0.4932672
5 MX1 42798749 0.0309253 0.0271947 0.1008781 0.5011366
13 MX1 42798847 0.1465303 0.1160429 0.1008781 0.5011366
141 HLA-DPB1 33048592 0.8785906 0.9471922 0.1008781 0.5011366
23 RNF39 30039206 0.1187244 0.1472846 0.1068671 0.5142981
151 UPK3B 76145628 0.7062744 0.7342650 0.1131272 0.5279269
133 HLA-DPB1 33048433 0.8554437 0.9256979 0.1324012 0.5869205
59 BRDT 92414650 0.4258523 0.3824652 0.1336017 0.5869205
145 IFITM1 312434 0.2057482 0.1337707 0.1395435 0.5869205
138 HLA-DPB1 33048571 0.8724026 0.9391389 0.1410134 0.5869205
128 FAM132A 1178105 0.9789670 0.9768675 0.1632381 0.6525123
20 RNF39 30039158 0.1019108 0.1247689 0.1737588 0.6525123
146 IFITM1 312463 0.1562166 0.1053054 0.1775117 0.6525123
24 RNF39 30039208 0.1471008 0.1726732 0.1827480 0.6525123
131 HLA-DPB1 33048417 0.8528855 0.9171898 0.1827480 0.6525123
132 HLA-DPB1 33048423 0.8696502 0.9347152 0.1827480 0.6525123
22 RNF39 30039202 0.1501742 0.1729478 0.1944141 0.6525123
152 UPK3B 76145620 0.7966523 0.8118123 0.2140627 0.6525123
144 IFITM1 312419 0.0729589 0.0619931 0.2220012 0.6525123
142 HLA-DPB1 33048602 0.4494760 0.6051056 0.2220643 0.6525123
18 RNF39 30039130 0.1422862 0.1686253 0.2327535 0.6525123
112 GFPT2 179740861 0.7560015 0.6917503 0.2327535 0.6525123
113 GFPT2 179740855 0.7807848 0.7143285 0.2327535 0.6525123
17 RNF39 30039127 0.3078670 0.3420550 0.2437936 0.6525123
52 HOOK2 12877099 0.2306115 0.2565141 0.2437936 0.6525123
63 BRDT 92414770 0.7509697 0.7249593 0.2437936 0.6525123
118 GFPT2 179740822 0.7419350 0.6747754 0.2437936 0.6525123
3 MX1 42798723 0.0513214 0.0468764 0.2551874 0.6525123
16 RNF39 30039123 0.3614561 0.3909412 0.2551874 0.6525123
116 GFPT2 179740832 0.7763586 0.7093739 0.2551874 0.6525123
64 BRDT 92414793 0.8320961 0.8058962 0.2634937 0.6525123
26 RNF39 30039235 0.1358569 0.1583816 0.2669368 0.6525123
42 RNF39 30039307 0.1733708 0.1928048 0.2669368 0.6525123
114 GFPT2 179740852 0.7368690 0.6748221 0.2669368 0.6525123
117 GFPT2 179740825 0.7798747 0.7096671 0.2669368 0.6525123
130 BRDT 92418017 0.9728535 0.9699854 0.2669368 0.6525123
115 GFPT2 179740840 0.7598012 0.6925568 0.2915099 0.7014458
110 GFPT2 179740869 0.7353703 0.6744261 0.3175214 0.7522814
81 TLR1 38805839 0.0596818 0.0494588 0.3267934 0.7625179
4 MX1 42798733 0.0346634 0.0322124 0.3449715 0.7903144
40 RNF39 30039278 0.3409712 0.3656945 0.3592338 0.7903144
54 HOOK2 12877138 0.2542766 0.2809405 0.3592338 0.7903144
123 FAM132A 1178172 0.8628519 0.8654238 0.3592338 0.7903144
19 RNF39 30039132 0.0922963 0.1037569 0.3738520 0.7996280
137 HLA-DPB1 33048549 0.8561483 0.9239807 0.3738520 0.7996280
134 HLA-DPB1 33048444 0.8251486 0.8968022 0.3888238 0.8091738
140 HLA-DPB1 33048581 0.8656858 0.9277086 0.3888238 0.8091738
38 RNF39 30039271 0.1879945 0.2014079 0.4041460 0.8163565
53 HOOK2 12877107 0.2337943 0.2575799 0.4041460 0.8163565
68 HELZ2 62199061 0.0356405 0.0448612 0.4081783 0.8163565
80 EIF2AK2 37383730 0.0263226 0.0247515 0.4319174 0.8389670
62 BRDT 92414751 0.7326712 0.7109765 0.4358270 0.8389670
120 FAM132A 1178202 0.7827009 0.7802450 0.4358270 0.8389670
126 FAM132A 1178136 0.9701882 0.9714783 0.4521770 0.8441006
47 RNF39 30039364 0.1044725 0.1073149 0.4688597 0.8441006
58 HOOK2 12877276 0.2590516 0.2859800 0.4688597 0.8441006
94 HOOK2 12876911 0.2628716 0.2962037 0.4858693 0.8441006
98 GFPT2 179740992 0.6312012 0.5793734 0.4858693 0.8441006
50 RNF39 30039418 0.4442470 0.4656233 0.5031992 0.8441006
82 HOOK2 12877020 0.2123525 0.2464723 0.5031992 0.8441006
92 HOOK2 12876926 0.2325951 0.2654917 0.5031992 0.8441006
97 GFPT2 179740994 0.6448891 0.5932223 0.5031992 0.8441006
104 GFPT2 179740935 0.6806278 0.6228022 0.5031992 0.8441006
43 RNF39 30039313 0.2053626 0.2208833 0.5208424 0.8441006
44 RNF39 30039323 0.2670671 0.2895114 0.5344638 0.8441006
71 GFPT2 179741067 0.5638664 0.5212852 0.5387912 0.8441006
111 GFPT2 179740867 0.7217714 0.6619451 0.5387912 0.8441006
153 UPK3B 76145606 0.3782685 0.3904465 0.5387912 0.8441006
154 UPK3B 76145589 0.1720512 0.1765031 0.5387912 0.8441006
35 SMAD3 67361821 0.8864407 0.8999875 0.5527815 0.8441006
49 RNF39 30039415 0.2266577 0.2420830 0.5570375 0.8441006
96 GFPT2 179740999 0.6234426 0.5743277 0.5570375 0.8441006
102 GFPT2 179740955 0.6733490 0.6193809 0.5570375 0.8441006
46 RNF39 30039354 0.2246827 0.2356277 0.5714019 0.8441006
48 RNF39 30039411 0.4167763 0.4355559 0.5755724 0.8441006
85 HOOK2 12876987 0.2186697 0.2531426 0.5755724 0.8441006
109 GFPT2 179740888 0.6252246 0.5673834 0.5755724 0.8441006
100 GFPT2 179740963 0.6543772 0.6027175 0.5943868 0.8441006
124 FAM132A 1178162 0.8130103 0.8095996 0.5943868 0.8441006
76 EIF2AK2 37383588 0.0759636 0.0681276 0.5975265 0.8441006
36 SMAD3 67361896 0.8435264 0.8366558 0.6134706 0.8441006
61 BRDT 92414719 0.3078300 0.2966023 0.6134706 0.8441006
95 GFPT2 179741008 0.5565324 0.5100013 0.6134706 0.8441006
101 GFPT2 179740957 0.6711285 0.6170463 0.6134706 0.8441006
74 GFPT2 179741042 0.4692564 0.4257726 0.6328136 0.8441006
91 HOOK2 12876937 0.2229114 0.2551046 0.6328136 0.8441006
93 HOOK2 12876918 0.2439106 0.2763449 0.6328136 0.8441006
107 GFPT2 179740906 0.6711654 0.6141981 0.6328136 0.8441006
148 UPK3B 76145702 0.2841578 0.2946057 0.6486972 0.8441006
41 RNF39 30039303 0.1915649 0.2016737 0.6524049 0.8441006
75 GFPT2 179741039 0.6135393 0.5627541 0.6524049 0.8441006
108 GFPT2 179740900 0.6263760 0.5783244 0.6524049 0.8441006
27 RNF39 30039239 0.3243063 0.3358206 0.6722331 0.8441006
103 GFPT2 179740940 0.6335832 0.5797049 0.6722331 0.8441006
106 GFPT2 179740918 0.6526585 0.5980296 0.6722331 0.8441006
79 EIF2AK2 37383713 0.0083365 0.0112373 0.6791509 0.8441006
70 GFPT2 179741081 0.5870507 0.5497762 0.6922864 0.8441006
105 GFPT2 179740920 0.6286866 0.5778832 0.6922864 0.8441006
119 FAM132A 1178207 0.8479868 0.8456628 0.6922864 0.8441006
39 RNF39 30039274 0.2086611 0.2208201 0.7125525 0.8441006
60 BRDT 92414661 0.5263980 0.5161855 0.7125525 0.8441006
72 GFPT2 179741063 0.5645206 0.5215559 0.7125525 0.8441006
99 GFPT2 179740970 0.5854953 0.5409305 0.7125525 0.8441006
73 GFPT2 179741060 0.6235241 0.5755289 0.7330186 0.8487584
87 HOOK2 12876948 0.2287765 0.2619367 0.7330186 0.8487584
90 HOOK2 12876942 0.2300281 0.2636881 0.7330186 0.8487584
150 UPK3B 76145689 0.3570678 0.3532317 0.7404102 0.8509192
77 EIF2AK2 37383623 0.0132245 0.0142002 0.7617952 0.8690108
57 HOOK2 12877235 0.3206069 0.3413112 0.7744984 0.8770056
143 IFI44L 79085647 0.1195439 0.1143348 0.7864803 0.8840727
127 FAM132A 1178118 0.9495490 0.9517401 0.7954847 0.8877148
78 EIF2AK2 37383679 0.0143214 0.0167932 0.8085050 0.8957537
55 HOOK2 12877201 0.2941553 0.3168446 0.8166164 0.8982780
121 FAM132A 1178192 0.9283732 0.9283924 0.8378791 0.9151304
56 HOOK2 12877215 0.2709562 0.2927520 0.8592579 0.9189286
69 GFPT2 179741101 0.5996110 0.5579517 0.8592579 0.9189286
89 HOOK2 12876944 0.2283631 0.2607402 0.8592579 0.9189286
88 HOOK2 12876946 0.2254400 0.2591300 0.8807380 0.9354045
122 FAM132A 1178182 0.7929911 0.7943505 0.9023041 0.9452709
149 UPK3B 76145693 0.5311877 0.5291985 0.9023041 0.9452709
45 RNF39 30039349 0.1943104 0.2053414 0.9120630 0.9490386
83 HOOK2 12876997 0.2060073 0.2361947 0.9456325 0.9708494
84 HOOK2 12876993 0.2152394 0.2462851 0.9456325 0.9708494
86 HOOK2 12876969 0.2234150 0.2551195 0.9891186 0.9955834
129 FAM132A 1178086 0.9193654 0.9182644 0.9891186 0.9955834
147 UPK3B 76145717 0.4323066 0.4356264 0.9891186 0.9955834
34 SMAD3 67361798 0.9058747 0.9061659 1.0000000 1.0000000

3.3.4.2 Figure15: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 15 in our analysis."

3.4 Validation of differential methylated CpGsites only in the validation stage due to the sequencing advantage in CD8+

3.4.1 Validation of differential methylated CpGsites between SSc patients and Controls

3.4.1.1 Table 18: The Differential methylated CpGsites between SSc patients and Controls

Gene Pos Mean.CD8.SSc Mean.CD8.NC P.value.CD8.SSC.NC FDR
15 MX1 42798863 0.2158335 0.2972670 0.0001326 0.0088424
12 MX1 42798837 0.1068262 0.1505124 0.0001555 0.0088424
14 MX1 42798857 0.1851206 0.2552752 0.0001820 0.0088424
9 MX1 42798816 0.1682997 0.2208034 0.0002297 0.0088424
11 MX1 42798829 0.1646297 0.2197405 0.0003753 0.0115607
13 MX1 42798847 0.1897550 0.2580407 0.0007640 0.0170880
8 MX1 42798813 0.1796408 0.2377021 0.0007767 0.0170880
10 MX1 42798818 0.1205289 0.1598394 0.0009838 0.0189387
7 MX1 42798781 0.1046483 0.1345820 0.0012065 0.0206453
4 MX1 42798733 0.0403381 0.0506473 0.0028125 0.0433129
78 EIF2AK2 37383679 0.0122648 0.0161317 0.0054003 0.0756042
50 RNF39 30039418 0.4389772 0.5283172 0.0063838 0.0819258
80 EIF2AK2 37383730 0.0248620 0.0340524 0.0095065 0.1126158
5 MX1 42798749 0.0357276 0.0423275 0.0125292 0.1378210
6 MX1 42798765 0.0408280 0.0470983 0.0176582 0.1812907
76 EIF2AK2 37383588 0.0946465 0.1141754 0.0206115 0.1983858
143 IFI44L 79085647 0.1689546 0.2059993 0.0238435 0.2159944
3 MX1 42798723 0.0614809 0.0700709 0.0286238 0.2448928
131 HLA-DPB1 33048417 0.9098175 0.9399218 0.0424526 0.3313670
48 RNF39 30039411 0.4391145 0.5018491 0.0441026 0.3313670
45 RNF39 30039349 0.2378623 0.3019271 0.0451864 0.3313670
141 HLA-DPB1 33048592 0.9288820 0.9615786 0.0495997 0.3380849
40 RNF39 30039278 0.3795850 0.4356661 0.0504932 0.3380849
44 RNF39 30039323 0.2883827 0.3438164 0.0560013 0.3593416
144 IFITM1 312419 0.0739377 0.1019998 0.0601917 0.3707811
139 HLA-DPB1 33048575 0.9252925 0.9567140 0.0768833 0.4398828
125 FAM132A 1178150 0.9022968 0.9091035 0.0771223 0.4398828
46 RNF39 30039354 0.2404657 0.3102584 0.0827823 0.4553024
42 RNF39 30039307 0.1729444 0.2349002 0.0895704 0.4631989
41 RNF39 30039303 0.2101137 0.2680066 0.0931316 0.4631989
77 EIF2AK2 37383623 0.0150487 0.0172126 0.0932413 0.4631989
134 HLA-DPB1 33048444 0.8794711 0.9096903 0.1006822 0.4845333
52 HOOK2 12877099 0.2279291 0.2514190 0.1055379 0.4925104
49 RNF39 30039415 0.2846470 0.3286858 0.1202159 0.5437163
43 RNF39 30039313 0.2371394 0.2898949 0.1235719 0.5437163
137 HLA-DPB1 33048549 0.9094355 0.9341162 0.1300042 0.5561291
51 IFITM1 313408 0.1764488 0.1866750 0.1370834 0.5705634
138 HLA-DPB1 33048571 0.9164888 0.9467651 0.1420384 0.5756292
136 HLA-DPB1 33048544 0.9300397 0.9584988 0.1461612 0.5771493
149 UPK3B 76145693 0.5685306 0.5530011 0.1517809 0.5843565
53 HOOK2 12877107 0.2314636 0.2541165 0.1804528 0.6658105
154 UPK3B 76145589 0.2019851 0.1890741 0.1815847 0.6658105
2 MX1 42798698 0.0415546 0.0458381 0.1860967 0.6664858
39 RNF39 30039274 0.2247512 0.2734733 0.1924404 0.6735413
151 UPK3B 76145628 0.7344427 0.7505882 0.2037455 0.6972625
1 MX1 42798695 0.0466905 0.0489980 0.2171385 0.7131396
150 UPK3B 76145689 0.4062791 0.3921679 0.2207433 0.7131396
146 IFITM1 312463 0.1395583 0.1586609 0.2222773 0.7131396
145 IFITM1 312434 0.1774891 0.1993537 0.2406777 0.7564156
47 RNF39 30039364 0.1515930 0.1401614 0.2495756 0.7686928
140 HLA-DPB1 33048581 0.9098786 0.9389990 0.2598686 0.7847012
128 FAM132A 1178105 0.9783984 0.9761999 0.2732366 0.8092007
68 HELZ2 62199061 0.0407535 0.0335129 0.2794895 0.8121017
133 HLA-DPB1 33048433 0.9232463 0.9465281 0.2959848 0.8441048
38 RNF39 30039271 0.2242318 0.2627923 0.3186390 0.8921893
69 GFPT2 179741101 0.5799309 0.5436586 0.3482935 0.9260539
105 GFPT2 179740920 0.5882954 0.5588129 0.3523922 0.9260539
54 HOOK2 12877138 0.2638735 0.2828210 0.3824304 0.9260539
25 RNF39 30039232 0.2572461 0.2765787 0.4031654 0.9260539
100 GFPT2 179740963 0.6021399 0.5755657 0.4117597 0.9260539
103 GFPT2 179740940 0.5820856 0.5537678 0.4169584 0.9260539
58 HOOK2 12877276 0.2465499 0.2671606 0.4174312 0.9260539
94 HOOK2 12876911 0.2798731 0.3049543 0.4277642 0.9260539
34 SMAD3 67361798 0.9372159 0.9274174 0.4290607 0.9260539
99 GFPT2 179740970 0.5475317 0.5222309 0.4381325 0.9260539
108 GFPT2 179740900 0.5866370 0.5621152 0.4435200 0.9260539
142 HLA-DPB1 33048602 0.5233596 0.5938896 0.4444654 0.9260539
107 GFPT2 179740906 0.6251411 0.5964526 0.4489448 0.9260539
37 HLA-DPB1 33048370 0.7327415 0.7459280 0.4544065 0.9260539
123 FAM132A 1178172 0.8245171 0.8278377 0.4628546 0.9260539
97 GFPT2 179740994 0.5941014 0.5692321 0.4766200 0.9260539
98 GFPT2 179740992 0.5831624 0.5598780 0.4822639 0.9260539
35 SMAD3 67361821 0.9348617 0.9361443 0.4828773 0.9260539
17 RNF39 30039127 0.3841659 0.3731225 0.4836774 0.9260539
62 BRDT 92414751 0.5075202 0.4788894 0.4857102 0.9260539
101 GFPT2 179740957 0.6177339 0.5937250 0.4879435 0.9260539
114 GFPT2 179740852 0.6846808 0.6570538 0.4994089 0.9260539
36 SMAD3 67361896 0.8997473 0.8938339 0.5025998 0.9260539
72 GFPT2 179741063 0.5353806 0.5105164 0.5032403 0.9260539
57 HOOK2 12877235 0.3506097 0.3714093 0.5040958 0.9260539
64 BRDT 92414793 0.5672853 0.5366430 0.5041728 0.9260539
102 GFPT2 179740955 0.6219072 0.5986114 0.5051942 0.9260539
106 GFPT2 179740918 0.6050829 0.5829248 0.5051942 0.9260539
111 GFPT2 179740867 0.6819934 0.6576121 0.5110143 0.9260539
126 FAM132A 1178136 0.9680554 0.9694773 0.5271179 0.9260539
95 GFPT2 179741008 0.5057461 0.4843944 0.5346363 0.9260539
96 GFPT2 179740999 0.5800966 0.5572977 0.5346363 0.9260539
104 GFPT2 179740935 0.6247533 0.5997596 0.5346363 0.9260539
109 GFPT2 179740888 0.5908451 0.5645584 0.5406258 0.9260539
31 COX7A2 75953937 0.1267371 0.1354768 0.5624329 0.9260539
19 RNF39 30039132 0.1526993 0.1601234 0.5683198 0.9260539
24 RNF39 30039208 0.2103395 0.2166896 0.5683219 0.9260539
33 COX7A2 75953974 0.2455319 0.2586032 0.5754383 0.9260539
71 GFPT2 179741067 0.5420300 0.5217057 0.5892100 0.9260539
110 GFPT2 179740869 0.6871845 0.6635659 0.5897022 0.9260539
70 GFPT2 179741081 0.5641737 0.5435904 0.5955982 0.9260539
55 HOOK2 12877201 0.3218085 0.3389160 0.5993194 0.9260539
28 COX7A2 75953821 0.0779455 0.0821239 0.6085513 0.9260539
30 COX7A2 75953883 0.1954050 0.2034265 0.6085513 0.9260539
152 UPK3B 76145620 0.8167159 0.8091339 0.6131467 0.9260539
112 GFPT2 179740861 0.7060889 0.6855562 0.6149784 0.9260539
67 COX7A2 75954122 0.4428005 0.4490352 0.6262348 0.9260539
74 GFPT2 179741042 0.4511989 0.4307610 0.6279970 0.9260539
115 GFPT2 179740840 0.7044013 0.6829977 0.6342391 0.9260539
63 BRDT 92414770 0.5137695 0.4928876 0.6427615 0.9260539
23 RNF39 30039206 0.2018929 0.2108971 0.6561120 0.9260539
113 GFPT2 179740855 0.7230183 0.7038407 0.6603041 0.9260539
73 GFPT2 179741060 0.5978390 0.5746584 0.6611208 0.9260539
118 GFPT2 179740822 0.6833521 0.6609020 0.6619679 0.9260539
147 UPK3B 76145717 0.4810049 0.4732804 0.6628272 0.9260539
32 COX7A2 75953960 0.2324648 0.2463432 0.6701641 0.9260539
116 GFPT2 179740832 0.7206030 0.6991309 0.6734937 0.9260539
130 BRDT 92418017 0.9733938 0.9726775 0.6818992 0.9293139
132 HLA-DPB1 33048423 0.9307672 0.9505762 0.6908851 0.9333009
26 RNF39 30039235 0.2392387 0.2488515 0.7086060 0.9398467
75 GFPT2 179741039 0.5938789 0.5738683 0.7086060 0.9398467
18 RNF39 30039130 0.2194435 0.2308035 0.7140394 0.9398467
60 BRDT 92414661 0.4234587 0.4071912 0.7279296 0.9459377
117 GFPT2 179740825 0.7180035 0.6970619 0.7340324 0.9459377
91 HOOK2 12876937 0.2342092 0.2565081 0.7418712 0.9459377
22 RNF39 30039202 0.2375842 0.2456934 0.7432367 0.9459377
83 HOOK2 12876997 0.2163085 0.2362756 0.7553705 0.9465025
129 FAM132A 1178086 0.9019360 0.8976444 0.7559727 0.9465025
79 EIF2AK2 37383713 0.0083446 0.0076138 0.7654747 0.9506702
65 COX7A2 75954022 0.5304357 0.5349920 0.7854763 0.9677068
16 RNF39 30039123 0.4574247 0.4575020 0.7925811 0.9687102
93 HOOK2 12876918 0.2571966 0.2814326 0.8100714 0.9751801
135 HLA-DPB1 33048542 0.0633443 0.0839724 0.8105393 0.9751801
84 HOOK2 12876993 0.2246503 0.2469626 0.8308391 0.9759680
86 HOOK2 12876969 0.2353652 0.2589791 0.8308391 0.9759680
124 FAM132A 1178162 0.7876508 0.7817024 0.8427612 0.9759680
87 HOOK2 12876948 0.2411423 0.2624347 0.8587098 0.9759680
56 HOOK2 12877215 0.2847495 0.3040664 0.8657062 0.9759680
119 FAM132A 1178207 0.8009946 0.8002057 0.8673836 0.9759680
27 RNF39 30039239 0.3921812 0.3984258 0.8710312 0.9759680
81 TLR1 38805839 0.0800520 0.0654668 0.8801208 0.9759680
153 UPK3B 76145606 0.4177201 0.4140856 0.8820041 0.9759680
90 HOOK2 12876942 0.2448346 0.2689455 0.8867558 0.9759680
20 RNF39 30039158 0.1617914 0.1669710 0.8893298 0.9759680
29 COX7A2 75953829 0.1900842 0.1911202 0.8896544 0.9759680
66 COX7A2 75954118 0.4763134 0.4770666 0.8935811 0.9759680
82 HOOK2 12877020 0.2262234 0.2465793 0.9078847 0.9846073
148 UPK3B 76145702 0.3201036 0.3185503 0.9260873 0.9848891
92 HOOK2 12876926 0.2451798 0.2694612 0.9290783 0.9848891
127 FAM132A 1178118 0.9413770 0.9412087 0.9334608 0.9848891
121 FAM132A 1178192 0.8986722 0.8958672 0.9374958 0.9848891
89 HOOK2 12876944 0.2412735 0.2659038 0.9503217 0.9848891
122 FAM132A 1178182 0.7394479 0.7345481 0.9521825 0.9848891
85 HOOK2 12876987 0.2314150 0.2545267 0.9574114 0.9848891
61 BRDT 92414719 0.2879416 0.2957146 0.9593076 0.9848891
120 FAM132A 1178202 0.7308277 0.7274506 0.9740981 0.9906631
21 RNF39 30039186 0.2308739 0.2303945 0.9777974 0.9906631
88 HOOK2 12876946 0.2385206 0.2610126 0.9857979 0.9922410
59 BRDT 92414650 0.3461574 0.3381310 0.9925983 0.9925983

3.4.1.2 Figure16: The Differential methylated CpGsites between SSc patients and Controls

[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD8+ T cells is 10"
[1] "Plot the figure of MX1 42798863"

[1] "Plot the figure of MX1 42798837"

[1] "Plot the figure of MX1 42798857"

[1] "Plot the figure of MX1 42798816"

[1] "Plot the figure of MX1 42798829"

[1] "Plot the figure of MX1 42798847"

[1] "Plot the figure of MX1 42798813"

[1] "Plot the figure of MX1 42798818"

[1] "Plot the figure of MX1 42798781"

[1] "Plot the figure of MX1 42798733"

3.4.2 Validation of differential methylated CpGsites between dcSSc patients and Controls

3.4.2.1 Table 19: The Differential methylated CpGsites between dcSSc patients and Controls

Gene Pos Mean.CD8.dc Mean.CD8.NC P.value.CD8.dc.NC FDR
151 UPK3B 76145628 0.7168508 0.7505882 0.0074676 0.6275811
137 HLA-DPB1 33048549 0.8846894 0.9341162 0.0357128 0.6275811
67 COX7A2 75954122 0.3900427 0.4490352 0.0404422 0.6275811
31 COX7A2 75953937 0.1020046 0.1354768 0.0412963 0.6275811
136 HLA-DPB1 33048544 0.9068650 0.9584988 0.0472206 0.6275811
30 COX7A2 75953883 0.1609718 0.2034265 0.0520467 0.6275811
65 COX7A2 75954022 0.4671704 0.5349920 0.0527722 0.6275811
50 RNF39 30039418 0.4424677 0.5283172 0.0575080 0.6275811
134 HLA-DPB1 33048444 0.8559200 0.9096903 0.0588658 0.6275811
40 RNF39 30039278 0.3615585 0.4356661 0.0600022 0.6275811
28 COX7A2 75953821 0.0618621 0.0821239 0.0622053 0.6275811
37 HLA-DPB1 33048370 0.6872302 0.7459280 0.0630489 0.6275811
133 HLA-DPB1 33048433 0.9009518 0.9465281 0.0678762 0.6275811
66 COX7A2 75954118 0.4232681 0.4770666 0.0738199 0.6275811
15 MX1 42798863 0.2567028 0.2972670 0.0801774 0.6275811
33 COX7A2 75953974 0.2048235 0.2586032 0.0803861 0.6275811
32 COX7A2 75953960 0.1962902 0.2463432 0.0837896 0.6275811
41 RNF39 30039303 0.1952517 0.2680066 0.0866138 0.6275811
141 HLA-DPB1 33048592 0.9067151 0.9615786 0.0870716 0.6275811
14 MX1 42798857 0.2210567 0.2552752 0.1085422 0.6275811
29 COX7A2 75953829 0.1553651 0.1911202 0.1109068 0.6275811
52 HOOK2 12877099 0.2162453 0.2514190 0.1208106 0.6275811
69 GFPT2 179741101 0.6244667 0.5436586 0.1356549 0.6275811
13 MX1 42798847 0.2248944 0.2580407 0.1380952 0.6275811
154 UPK3B 76145589 0.2005878 0.1890741 0.1405363 0.6275811
45 RNF39 30039349 0.2382702 0.3019271 0.1506938 0.6275811
128 FAM132A 1178105 0.9793370 0.9761999 0.1506938 0.6275811
131 HLA-DPB1 33048417 0.8982112 0.9399218 0.1541931 0.6275811
125 FAM132A 1178150 0.9015033 0.9091035 0.1559733 0.6275811
53 HOOK2 12877107 0.2193410 0.2541165 0.1627761 0.6275811
12 MX1 42798837 0.1306970 0.1505124 0.1648895 0.6275811
74 GFPT2 179741042 0.5025036 0.4307610 0.1669421 0.6275811
44 RNF39 30039323 0.2900312 0.3438164 0.1854975 0.6275811
99 GFPT2 179740970 0.5887988 0.5222309 0.1938575 0.6275811
48 RNF39 30039411 0.4398426 0.5018491 0.1946962 0.6275811
11 MX1 42798829 0.2007530 0.2197405 0.2000648 0.6275811
114 GFPT2 179740852 0.7266582 0.6570538 0.2064129 0.6275811
149 UPK3B 76145693 0.5693504 0.5530011 0.2097935 0.6275811
105 GFPT2 179740920 0.6355716 0.5588129 0.2129027 0.6275811
71 GFPT2 179741067 0.5889373 0.5217057 0.2164994 0.6275811
107 GFPT2 179740906 0.6717459 0.5964526 0.2195354 0.6275811
108 GFPT2 179740900 0.6291681 0.5621152 0.2195354 0.6275811
102 GFPT2 179740955 0.6632321 0.5986114 0.2263120 0.6275811
109 GFPT2 179740888 0.6393397 0.5645584 0.2263120 0.6275811
70 GFPT2 179741081 0.6102137 0.5435904 0.2303608 0.6275811
72 GFPT2 179741063 0.5838811 0.5105164 0.2303608 0.6275811
46 RNF39 30039354 0.2384689 0.3102584 0.2312846 0.6275811
100 GFPT2 179740963 0.6408295 0.5755657 0.2332332 0.6275811
103 GFPT2 179740940 0.6219964 0.5537678 0.2332332 0.6275811
112 GFPT2 179740861 0.7475890 0.6855562 0.2332332 0.6275811
9 MX1 42798816 0.2059071 0.2208034 0.2475131 0.6275811
8 MX1 42798813 0.2192756 0.2377021 0.2548731 0.6275811
104 GFPT2 179740935 0.6658861 0.5997596 0.2548731 0.6275811
106 GFPT2 179740918 0.6521347 0.5829248 0.2548731 0.6275811
116 GFPT2 179740832 0.7624362 0.6991309 0.2548731 0.6275811
75 GFPT2 179741039 0.6485978 0.5738683 0.2599069 0.6275811
97 GFPT2 179740994 0.6334668 0.5692321 0.2623807 0.6275811
101 GFPT2 179740957 0.6589853 0.5937250 0.2623807 0.6275811
110 GFPT2 179740869 0.7297972 0.6635659 0.2623807 0.6275811
111 GFPT2 179740867 0.7258763 0.6576121 0.2623807 0.6275811
113 GFPT2 179740855 0.7636966 0.7038407 0.2623807 0.6275811
49 RNF39 30039415 0.2872570 0.3286858 0.2725096 0.6275811
25 RNF39 30039232 0.2412211 0.2765787 0.2756029 0.6275811
43 RNF39 30039313 0.2391492 0.2898949 0.2836834 0.6275811
95 GFPT2 179741008 0.5458332 0.4843944 0.2857937 0.6275811
98 GFPT2 179740992 0.6218308 0.5598780 0.2857937 0.6275811
117 GFPT2 179740825 0.7615307 0.6970619 0.2857937 0.6275811
79 EIF2AK2 37383713 0.0118696 0.0076138 0.2890215 0.6275811
7 MX1 42798781 0.1233523 0.1345820 0.2938959 0.6275811
150 UPK3B 76145689 0.4091882 0.3921679 0.2969910 0.6275811
96 GFPT2 179740999 0.6203808 0.5572977 0.3021474 0.6275811
115 GFPT2 179740840 0.7503077 0.6829977 0.3021474 0.6275811
24 RNF39 30039208 0.1906980 0.2166896 0.3054799 0.6275811
39 RNF39 30039274 0.2189513 0.2734733 0.3088587 0.6275811
42 RNF39 30039307 0.1771945 0.2349002 0.3175620 0.6275811
4 MX1 42798733 0.0449783 0.0506473 0.3199628 0.6275811
118 GFPT2 179740822 0.7255467 0.6609020 0.3199628 0.6275811
142 HLA-DPB1 33048602 0.4550854 0.5938896 0.3199802 0.6275811
57 HOOK2 12877235 0.3353043 0.3714093 0.3250936 0.6275811
38 RNF39 30039271 0.2125212 0.2627923 0.3264212 0.6275811
58 HOOK2 12877276 0.2293970 0.2671606 0.3335584 0.6275811
76 EIF2AK2 37383588 0.1093809 0.1141754 0.3341666 0.6275811
80 EIF2AK2 37383730 0.0288894 0.0340524 0.3398926 0.6296494
73 GFPT2 179741060 0.6451812 0.5746584 0.3446061 0.6296494
139 HLA-DPB1 33048575 0.9091051 0.9567140 0.3475338 0.6296494
143 IFI44L 79085647 0.1747650 0.2059993 0.3578290 0.6407635
23 RNF39 30039206 0.1813594 0.2108971 0.3634106 0.6432786
138 HLA-DPB1 33048571 0.9044165 0.9467651 0.3753325 0.6568318
10 MX1 42798818 0.1505739 0.1598394 0.3831169 0.6629214
121 FAM132A 1178192 0.8928645 0.8958672 0.3927697 0.6720725
3 MX1 42798723 0.0658323 0.0700709 0.4027320 0.6815465
68 HELZ2 62199061 0.0389775 0.0335129 0.4176932 0.6991821
54 HOOK2 12877138 0.2519799 0.2828210 0.4356765 0.7214427
17 RNF39 30039127 0.3894824 0.3731225 0.4516335 0.7399103
22 RNF39 30039202 0.2191423 0.2456934 0.4665199 0.7562533
26 RNF39 30039235 0.2208101 0.2488515 0.5002878 0.7891718
123 FAM132A 1178172 0.8193061 0.8278377 0.5002878 0.7891718
129 FAM132A 1178086 0.9048460 0.8976444 0.5079658 0.7891718
1 MX1 42798695 0.0521433 0.0489980 0.5092635 0.7891718
132 HLA-DPB1 33048423 0.9132301 0.9505762 0.5196934 0.7891718
119 FAM132A 1178207 0.8051401 0.8002057 0.5255572 0.7891718
135 HLA-DPB1 33048542 0.0688653 0.0839724 0.5331882 0.7891718
140 HLA-DPB1 33048581 0.8955914 0.9389990 0.5334663 0.7891718
56 HOOK2 12877215 0.2742889 0.3040664 0.5421412 0.7891718
27 RNF39 30039239 0.3743278 0.3984258 0.5434550 0.7891718
20 RNF39 30039158 0.1510334 0.1669710 0.5472100 0.7891718
91 HOOK2 12876937 0.2200042 0.2565081 0.5534452 0.7891718
94 HOOK2 12876911 0.2664089 0.3049543 0.5534452 0.7891718
147 UPK3B 76145717 0.4805704 0.4732804 0.5592647 0.7901538
51 IFITM1 313408 0.1861145 0.1866750 0.5837457 0.8098814
126 FAM132A 1178136 0.9681518 0.9694773 0.5837457 0.8098814
34 SMAD3 67361798 0.9436187 0.9274174 0.6042510 0.8308451
62 BRDT 92414751 0.5054684 0.4788894 0.6213551 0.8468025
55 HOOK2 12877201 0.3137922 0.3389160 0.6477159 0.8680289
19 RNF39 30039132 0.1468104 0.1601234 0.6502388 0.8680289
89 HOOK2 12876944 0.2273296 0.2659038 0.6599430 0.8680289
64 BRDT 92414793 0.5605071 0.5366430 0.6699389 0.8680289
127 FAM132A 1178118 0.9435336 0.9412087 0.6765643 0.8680289
60 BRDT 92414661 0.4353187 0.4071912 0.6832095 0.8680289
87 HOOK2 12876948 0.2284571 0.2624347 0.6846633 0.8680289
120 FAM132A 1178202 0.7223557 0.7274506 0.6862044 0.8680289
78 EIF2AK2 37383679 0.0151014 0.0161317 0.6876593 0.8680289
36 SMAD3 67361896 0.9011689 0.8938339 0.7036189 0.8809537
5 MX1 42798749 0.0419203 0.0423275 0.7185415 0.8923822
153 UPK3B 76145606 0.4234001 0.4140856 0.7303898 0.8970734
152 UPK3B 76145620 0.8073974 0.8091339 0.7372189 0.8970734
148 UPK3B 76145702 0.3263160 0.3185503 0.7397943 0.8970734
61 BRDT 92414719 0.3011353 0.2957146 0.7647386 0.9145581
144 IFITM1 312419 0.0919347 0.1019998 0.7721429 0.9145581
124 FAM132A 1178162 0.7826432 0.7817024 0.7808315 0.9145581
35 SMAD3 67361821 0.9322478 0.9361443 0.7834223 0.9145581
47 RNF39 30039364 0.1371199 0.1401614 0.7946507 0.9145581
146 IFITM1 312463 0.1617244 0.1586609 0.7967807 0.9145581
6 MX1 42798765 0.0488478 0.0470983 0.7988268 0.9145581
18 RNF39 30039130 0.2177503 0.2308035 0.8065675 0.9145581
82 HOOK2 12877020 0.2134993 0.2465793 0.8128033 0.9145581
63 BRDT 92414770 0.5120284 0.4928876 0.8136004 0.9145581
85 HOOK2 12876987 0.2178240 0.2545267 0.8259565 0.9217195
88 HOOK2 12876946 0.2236624 0.2610126 0.8391577 0.9297143
59 BRDT 92414650 0.3600865 0.3381310 0.8560755 0.9416830
122 FAM132A 1178182 0.7392234 0.7345481 0.8646147 0.9443310
92 HOOK2 12876926 0.2311439 0.2694612 0.8923717 0.9652470
81 TLR1 38805839 0.0862660 0.0654668 0.9004698 0.9652470
86 HOOK2 12876969 0.2223231 0.2589791 0.9057593 0.9652470
130 BRDT 92418017 0.9714090 0.9726775 0.9151402 0.9652470
84 HOOK2 12876993 0.2123469 0.2469626 0.9191733 0.9652470
21 RNF39 30039186 0.2219051 0.2303945 0.9213721 0.9652470
83 HOOK2 12876997 0.2033761 0.2362756 0.9326098 0.9670314
16 RNF39 30039123 0.4496789 0.4575020 0.9356343 0.9670314
77 EIF2AK2 37383623 0.0174223 0.0172126 0.9627358 0.9841293
2 MX1 42798698 0.0454972 0.0458381 0.9649580 0.9841293
90 HOOK2 12876942 0.2311652 0.2689455 0.9865068 0.9936200
145 IFITM1 312434 0.2011502 0.1993537 0.9871679 0.9936200
93 HOOK2 12876918 0.2415910 0.2814326 1.0000000 1.0000000

3.4.2.2 Figure17: The Differential methylated CpGsites between dcSSc patients and Controls

[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 17 in our analysis."

3.4.3 Validation of differential methylated CpGsites between lcSSc patients and Controls

3.4.3.1 Table 20: The Differential methylated CpGsites between lcSSc patients and Controls

Gene Pos Mean.CD8.lc Mean.CD8.NC P.value.CD8.lc.NC FDR
9 MX1 42798816 0.1451567 0.2208034 0.0000090 0.0008554
12 MX1 42798837 0.0921364 0.1505124 0.0000111 0.0008554
14 MX1 42798857 0.1630061 0.2552752 0.0000323 0.0010596
15 MX1 42798863 0.1906832 0.2972670 0.0000323 0.0010596
11 MX1 42798829 0.1424000 0.2197405 0.0000344 0.0010596
10 MX1 42798818 0.1020396 0.1598394 0.0000444 0.0011384
8 MX1 42798813 0.1552502 0.2377021 0.0000918 0.0020185
7 MX1 42798781 0.0931382 0.1345820 0.0001174 0.0022595
13 MX1 42798847 0.1681307 0.2580407 0.0002393 0.0038048
78 EIF2AK2 37383679 0.0105629 0.0161317 0.0002471 0.0038048
4 MX1 42798733 0.0374825 0.0506473 0.0003426 0.0047968
6 MX1 42798765 0.0358928 0.0470983 0.0003930 0.0050436
5 MX1 42798749 0.0319166 0.0423275 0.0009652 0.0114337
80 EIF2AK2 37383730 0.0224456 0.0340524 0.0032162 0.0353777
76 EIF2AK2 37383588 0.0858059 0.1141754 0.0107400 0.1102637
143 IFI44L 79085647 0.1654684 0.2059993 0.0120053 0.1123128
3 MX1 42798723 0.0588032 0.0700709 0.0130194 0.1123128
50 RNF39 30039418 0.4368291 0.5283172 0.0131275 0.1123128
144 IFITM1 312419 0.0633512 0.1019998 0.0166821 0.1352131
77 EIF2AK2 37383623 0.0136245 0.0172126 0.0199767 0.1538209
1 MX1 42798695 0.0433350 0.0489980 0.0255921 0.1876758
48 RNF39 30039411 0.4386664 0.5018491 0.0570498 0.3992447
146 IFITM1 312463 0.1273669 0.1586609 0.0626705 0.3992447
2 MX1 42798698 0.0391284 0.0458381 0.0664892 0.3992447
47 RNF39 30039364 0.1604995 0.1401614 0.0669090 0.3992447
131 HLA-DPB1 33048417 0.9160670 0.9399218 0.0674049 0.3992447
139 HLA-DPB1 33048575 0.9340088 0.9567140 0.0727966 0.4139094
45 RNF39 30039349 0.2376113 0.3019271 0.0752563 0.4139094
44 RNF39 30039323 0.2873683 0.3438164 0.0820504 0.4357160
51 IFITM1 313408 0.1705007 0.1866750 0.0893258 0.4585393
42 RNF39 30039307 0.1703290 0.2349002 0.0955803 0.4748180
145 IFITM1 312434 0.1643440 0.1993537 0.1029896 0.4956375
46 RNF39 30039354 0.2416944 0.3102584 0.1142521 0.5331762
141 HLA-DPB1 33048592 0.9408180 0.9615786 0.1210582 0.5483223
125 FAM132A 1178150 0.9027851 0.9091035 0.1442609 0.6347479
138 HLA-DPB1 33048571 0.9229893 0.9467651 0.1564542 0.6484039
49 RNF39 30039415 0.2830408 0.3286858 0.1622257 0.6484039
40 RNF39 30039278 0.3906782 0.4356661 0.1633218 0.6484039
43 RNF39 30039313 0.2359025 0.2898949 0.1642062 0.6484039
79 EIF2AK2 37383713 0.0062297 0.0076138 0.2353836 0.9062268
52 HOOK2 12877099 0.2355685 0.2514190 0.2514498 0.9216707
41 RNF39 30039303 0.2192596 0.2680066 0.2590672 0.9216707
140 HLA-DPB1 33048581 0.9175717 0.9389990 0.2610302 0.9216707
149 UPK3B 76145693 0.5680260 0.5530011 0.2674674 0.9216707
39 RNF39 30039274 0.2283204 0.2734733 0.2731704 0.9216707
66 COX7A2 75954118 0.5089567 0.4770666 0.2753042 0.9216707
65 COX7A2 75954022 0.5693682 0.5349920 0.3177918 0.9911496
134 HLA-DPB1 33048444 0.8921524 0.9096903 0.3215650 0.9911496
150 UPK3B 76145689 0.4044889 0.3921679 0.3314886 0.9911496
152 UPK3B 76145620 0.8224503 0.8091339 0.3372318 0.9911496
29 COX7A2 75953829 0.2109157 0.1911202 0.3512707 0.9911496
68 HELZ2 62199061 0.0418837 0.0335129 0.3524144 0.9911496
53 HOOK2 12877107 0.2393899 0.2541165 0.3877290 0.9911496
154 UPK3B 76145589 0.2028450 0.1890741 0.4158312 0.9911496
67 COX7A2 75954122 0.4752669 0.4490352 0.4375967 0.9911496
35 SMAD3 67361821 0.9362776 0.9361443 0.4445705 0.9911496
34 SMAD3 67361798 0.9337478 0.9274174 0.4697180 0.9911496
38 RNF39 30039271 0.2314384 0.2627923 0.4935262 0.9911496
94 HOOK2 12876911 0.2886766 0.3049543 0.4938880 0.9911496
137 HLA-DPB1 33048549 0.9227604 0.9341162 0.4983199 0.9911496
136 HLA-DPB1 33048544 0.9425184 0.9584988 0.5025949 0.9911496
54 HOOK2 12877138 0.2716501 0.2828210 0.5102116 0.9911496
130 BRDT 92418017 0.9746152 0.9726775 0.5102116 0.9911496
36 SMAD3 67361896 0.8989773 0.8938339 0.5149527 0.9911496
30 COX7A2 75953883 0.2160649 0.2034265 0.5158519 0.9911496
64 BRDT 92414793 0.5714565 0.5366430 0.5287412 0.9911496
31 COX7A2 75953937 0.1415766 0.1354768 0.5333464 0.9911496
32 COX7A2 75953960 0.2541696 0.2463432 0.5333464 0.9911496
62 BRDT 92414751 0.5087828 0.4788894 0.5356710 0.9911496
28 COX7A2 75953821 0.0875956 0.0821239 0.5511314 0.9911496
123 FAM132A 1178172 0.8277238 0.8278377 0.5884961 0.9911496
121 FAM132A 1178192 0.9022461 0.8958672 0.6157679 0.9911496
128 FAM132A 1178105 0.9778209 0.9761999 0.6157679 0.9911496
126 FAM132A 1178136 0.9679960 0.9694773 0.6249785 0.9911496
63 BRDT 92414770 0.5148409 0.4928876 0.6342472 0.9911496
19 RNF39 30039132 0.1563233 0.1601234 0.6366151 0.9911496
33 COX7A2 75953974 0.2699570 0.2586032 0.6537553 0.9911496
17 RNF39 30039127 0.3808942 0.3731225 0.6602062 0.9911496
58 HOOK2 12877276 0.2577653 0.2671606 0.6685840 0.9911496
127 FAM132A 1178118 0.9400499 0.9412087 0.6718784 0.9911496
55 HOOK2 12877201 0.3270499 0.3389160 0.6873059 0.9911496
105 GFPT2 179740920 0.5592024 0.5588129 0.6873059 0.9911496
84 HOOK2 12876993 0.2326949 0.2469626 0.6967390 0.9911496
25 RNF39 30039232 0.2671077 0.2765787 0.7006501 0.9911496
148 UPK3B 76145702 0.3162807 0.3185503 0.7035164 0.9911496
142 HLA-DPB1 33048602 0.5601226 0.5938896 0.7062118 0.9911496
83 HOOK2 12876997 0.2247642 0.2362756 0.7062186 0.9911496
82 HOOK2 12877020 0.2345430 0.2465793 0.7253119 0.9911496
93 HOOK2 12876918 0.2674003 0.2814326 0.7349230 0.9911496
18 RNF39 30039130 0.2204855 0.2308035 0.7378947 0.9911496
16 RNF39 30039123 0.4621913 0.4575020 0.7594439 0.9911496
74 GFPT2 179741042 0.4196268 0.4307610 0.7594439 0.9911496
61 BRDT 92414719 0.2798224 0.2957146 0.7677854 0.9911496
100 GFPT2 179740963 0.5783309 0.5755657 0.7737639 0.9911496
117 GFPT2 179740825 0.6912174 0.6970619 0.7737639 0.9911496
75 GFPT2 179741039 0.5602058 0.5738683 0.7793699 0.9911496
37 HLA-DPB1 33048370 0.7607485 0.7459280 0.7835663 0.9911496
103 GFPT2 179740940 0.5575250 0.5537678 0.7835663 0.9911496
85 HOOK2 12876987 0.2403014 0.2545267 0.8032715 0.9911496
120 FAM132A 1178202 0.7360413 0.7274506 0.8081759 0.9911496
69 GFPT2 179741101 0.5525242 0.5436586 0.8095248 0.9911496
89 HOOK2 12876944 0.2503907 0.2659038 0.8131714 0.9911496
92 HOOK2 12876926 0.2543572 0.2694612 0.8131714 0.9911496
20 RNF39 30039158 0.1684117 0.1669710 0.8132633 0.9911496
90 HOOK2 12876942 0.2537722 0.2689455 0.8231007 0.9911496
116 GFPT2 179740832 0.6948595 0.6991309 0.8231007 0.9911496
133 HLA-DPB1 33048433 0.9352510 0.9465281 0.8286707 0.9911496
119 FAM132A 1178207 0.7984435 0.8002057 0.8297871 0.9911496
122 FAM132A 1178182 0.7395861 0.7345481 0.8297871 0.9911496
56 HOOK2 12877215 0.2915891 0.3040664 0.8330581 0.9911496
57 HOOK2 12877235 0.3606170 0.3714093 0.8330581 0.9911496
86 HOOK2 12876969 0.2438928 0.2589791 0.8330581 0.9911496
98 GFPT2 179740992 0.5593665 0.5598780 0.8330581 0.9911496
27 RNF39 30039239 0.4031679 0.3984258 0.8388078 0.9911496
60 BRDT 92414661 0.4161603 0.4071912 0.8490843 0.9911496
97 GFPT2 179740994 0.5698766 0.5692321 0.8530507 0.9911496
108 GFPT2 179740900 0.5604640 0.5621152 0.8530507 0.9911496
113 GFPT2 179740855 0.6979854 0.7038407 0.8530507 0.9911496
147 UPK3B 76145717 0.4812723 0.4732804 0.8542274 0.9911496
107 GFPT2 179740906 0.5964612 0.5964526 0.8630829 0.9911496
101 GFPT2 179740957 0.5923485 0.5937250 0.8731368 0.9911496
59 BRDT 92414650 0.3375857 0.3381310 0.8809049 0.9911496
99 GFPT2 179740970 0.5221365 0.5222309 0.8832110 0.9911496
112 GFPT2 179740861 0.6805505 0.6855562 0.8832110 0.9911496
151 UPK3B 76145628 0.7452686 0.7505882 0.8955871 0.9911496
71 GFPT2 179741067 0.5131640 0.5217057 0.9015021 0.9911496
88 HOOK2 12876946 0.2482356 0.2610126 0.9034137 0.9911496
96 GFPT2 179740999 0.5553063 0.5572977 0.9034137 0.9911496
21 RNF39 30039186 0.2363932 0.2303945 0.9059812 0.9911496
132 HLA-DPB1 33048423 0.9402103 0.9505762 0.9110651 0.9911496
70 GFPT2 179741081 0.5358414 0.5435904 0.9118262 0.9911496
106 GFPT2 179740918 0.5761280 0.5829248 0.9135391 0.9911496
111 GFPT2 179740867 0.6549886 0.6576121 0.9135391 0.9911496
95 GFPT2 179741008 0.4810771 0.4843944 0.9236783 0.9911496
118 GFPT2 179740822 0.6573863 0.6609020 0.9236783 0.9911496
81 TLR1 38805839 0.0720627 0.0654668 0.9301954 0.9911496
135 HLA-DPB1 33048542 0.0603714 0.0839724 0.9387683 0.9911496
72 GFPT2 179741063 0.5055341 0.5105164 0.9428796 0.9911496
124 FAM132A 1178162 0.7907324 0.7817024 0.9428796 0.9911496
115 GFPT2 179740840 0.6761512 0.6829977 0.9439917 0.9911496
24 RNF39 30039208 0.2224265 0.2166896 0.9529086 0.9911496
22 RNF39 30039202 0.2489331 0.2456934 0.9532521 0.9911496
73 GFPT2 179741060 0.5687054 0.5746584 0.9532521 0.9911496
102 GFPT2 179740955 0.5964764 0.5986114 0.9541628 0.9911496
87 HOOK2 12876948 0.2494365 0.2624347 0.9643412 0.9911496
104 GFPT2 179740935 0.5994408 0.5997596 0.9643412 0.9911496
110 GFPT2 179740869 0.6609613 0.6635659 0.9643412 0.9911496
129 FAM132A 1178086 0.9001452 0.8976444 0.9738276 0.9911496
26 RNF39 30039235 0.2505794 0.2488515 0.9740188 0.9911496
153 UPK3B 76145606 0.4142247 0.4140856 0.9740188 0.9911496
114 GFPT2 179740852 0.6588486 0.6570538 0.9745253 0.9911496
23 RNF39 30039206 0.2145289 0.2108971 0.9790607 0.9911496
91 HOOK2 12876937 0.2434971 0.2565081 0.9847136 0.9911496
109 GFPT2 179740888 0.5610022 0.5645584 0.9949042 0.9949042

3.4.3.2 Figure18: The Differential methylated CpGsites between lcSSc patients and Controls

[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD8+ T cells is 14"
[1] "Plot the figure of MX1 42798816"

[1] "Plot the figure of MX1 42798837"

[1] "Plot the figure of MX1 42798857"

[1] "Plot the figure of MX1 42798863"

[1] "Plot the figure of MX1 42798829"

[1] "Plot the figure of MX1 42798818"

[1] "Plot the figure of MX1 42798813"

[1] "Plot the figure of MX1 42798781"

[1] "Plot the figure of MX1 42798847"

[1] "Plot the figure of EIF2AK2 37383679"

[1] "Plot the figure of MX1 42798733"

[1] "Plot the figure of MX1 42798765"

[1] "Plot the figure of MX1 42798749"

[1] "Plot the figure of EIF2AK2 37383730"

3.4.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients

3.4.4.1 Table 21: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

Gene Pos Mean.CD8.dc Mean.CD8.lc P.value.CD8.dc.lc FDR
6 MX1 42798765 0.0488478 0.0358928 0.0099600 0.2785737
66 COX7A2 75954118 0.4232681 0.5089567 0.0112671 0.2785737
11 MX1 42798829 0.2007530 0.1424000 0.0121899 0.2785737
10 MX1 42798818 0.1505739 0.1020396 0.0131771 0.2785737
65 COX7A2 75954022 0.4671704 0.5693682 0.0131771 0.2785737
30 COX7A2 75953883 0.1609718 0.2160649 0.0149799 0.2785737
67 COX7A2 75954122 0.3900427 0.4752669 0.0184208 0.2785737
9 MX1 42798816 0.2059071 0.1451567 0.0222112 0.2785737
12 MX1 42798837 0.1306970 0.0921364 0.0222112 0.2785737
31 COX7A2 75953937 0.1020046 0.1415766 0.0241357 0.2785737
8 MX1 42798813 0.2192756 0.1552502 0.0255997 0.2785737
15 MX1 42798863 0.2567028 0.1906832 0.0255997 0.2785737
79 EIF2AK2 37383713 0.0118696 0.0062297 0.0260472 0.2785737
7 MX1 42798781 0.1233523 0.0931382 0.0274510 0.2785737
14 MX1 42798857 0.2210567 0.1630061 0.0274510 0.2785737
5 MX1 42798749 0.0419203 0.0319166 0.0314925 0.2785737
29 COX7A2 75953829 0.1553651 0.2109157 0.0325606 0.2785737
33 COX7A2 75953974 0.2048235 0.2699570 0.0325606 0.2785737
37 HLA-DPB1 33048370 0.6872302 0.7607485 0.0360196 0.2896434
32 COX7A2 75953960 0.1962902 0.2541696 0.0376160 0.2896434
78 EIF2AK2 37383679 0.0151014 0.0105629 0.0433046 0.3175667
28 COX7A2 75953821 0.0618621 0.0875956 0.0464036 0.3248253
1 MX1 42798695 0.0521433 0.0433350 0.0505153 0.3382332
151 UPK3B 76145628 0.7168508 0.7452686 0.0536474 0.3442377
13 MX1 42798847 0.2248944 0.1681307 0.0758536 0.4636141
77 EIF2AK2 37383623 0.0174223 0.0136245 0.0782725 0.4636141
144 IFITM1 312419 0.0919347 0.0633512 0.0826675 0.4715109
80 EIF2AK2 37383730 0.0288894 0.0224456 0.0884798 0.4866390
2 MX1 42798698 0.0454972 0.0391284 0.1060290 0.5630507
47 RNF39 30039364 0.1371199 0.1604995 0.1118556 0.5741920
4 MX1 42798733 0.0449783 0.0374825 0.1179255 0.5858232
74 GFPT2 179741042 0.5025036 0.4196268 0.1308176 0.6295596
133 HLA-DPB1 33048433 0.9009518 0.9352510 0.1604089 0.6881031
75 GFPT2 179741039 0.6485978 0.5602058 0.1676838 0.6881031
121 FAM132A 1178192 0.8928645 0.9022461 0.1758912 0.6881031
137 HLA-DPB1 33048549 0.8846894 0.9227604 0.1779858 0.6881031
3 MX1 42798723 0.0658323 0.0588032 0.1931756 0.6881031
70 GFPT2 179741081 0.6102137 0.5358414 0.1931756 0.6881031
76 EIF2AK2 37383588 0.1093809 0.0858059 0.2013287 0.6881031
113 GFPT2 179740855 0.7636966 0.6979854 0.2022604 0.6881031
51 IFITM1 313408 0.1861145 0.1705007 0.2116451 0.6881031
112 GFPT2 179740861 0.7475890 0.6805505 0.2116451 0.6881031
114 GFPT2 179740852 0.7266582 0.6588486 0.2116451 0.6881031
109 GFPT2 179740888 0.6393397 0.5610022 0.2213328 0.6881031
71 GFPT2 179741067 0.5889373 0.5131640 0.2313265 0.6881031
115 GFPT2 179740840 0.7503077 0.6761512 0.2313265 0.6881031
116 GFPT2 179740832 0.7624362 0.6948595 0.2416289 0.6881031
117 GFPT2 179740825 0.7615307 0.6912174 0.2416289 0.6881031
146 IFITM1 312463 0.1617244 0.1273669 0.2436558 0.6881031
111 GFPT2 179740867 0.7258763 0.6549886 0.2522421 0.6881031
118 GFPT2 179740822 0.7255467 0.6573863 0.2522421 0.6881031
145 IFITM1 312434 0.2011502 0.1643440 0.2597877 0.6881031
107 GFPT2 179740906 0.6717459 0.5964612 0.2631682 0.6881031
128 FAM132A 1178105 0.9793370 0.9778209 0.2631682 0.6881031
72 GFPT2 179741063 0.5838811 0.5055341 0.2744087 0.6881031
104 GFPT2 179740935 0.6658861 0.5994408 0.2744087 0.6881031
108 GFPT2 179740900 0.6291681 0.5604640 0.2744087 0.6881031
110 GFPT2 179740869 0.7297972 0.6609613 0.2744087 0.6881031
136 HLA-DPB1 33048544 0.9068650 0.9425184 0.2748689 0.6881031
152 UPK3B 76145620 0.8073974 0.8224503 0.2824113 0.6881031
73 GFPT2 179741060 0.6451812 0.5687054 0.2859649 0.6881031
95 GFPT2 179741008 0.5458332 0.4810771 0.2859649 0.6881031
105 GFPT2 179740920 0.6355716 0.5592024 0.2859649 0.6881031
106 GFPT2 179740918 0.6521347 0.5761280 0.2859649 0.6881031
134 HLA-DPB1 33048444 0.8559200 0.8921524 0.2940729 0.6967267
99 GFPT2 179740970 0.5887988 0.5221365 0.3225341 0.7525795
23 RNF39 30039206 0.1813594 0.2145289 0.3484969 0.7741731
69 GFPT2 179741101 0.6244667 0.5525242 0.3484969 0.7741731
96 GFPT2 179740999 0.6203808 0.5553063 0.3484969 0.7741731
97 GFPT2 179740994 0.6334668 0.5698766 0.3619511 0.7741731
101 GFPT2 179740957 0.6589853 0.5923485 0.3619511 0.7741731
102 GFPT2 179740955 0.6632321 0.5964764 0.3619511 0.7741731
20 RNF39 30039158 0.1510334 0.1684117 0.3757183 0.7926113
25 RNF39 30039232 0.2412211 0.2671077 0.4188760 0.8540057
119 FAM132A 1178207 0.8051401 0.7984435 0.4188760 0.8540057
100 GFPT2 179740963 0.6408295 0.5783309 0.4338707 0.8540057
103 GFPT2 179740940 0.6219964 0.5575250 0.4338707 0.8540057
127 FAM132A 1178118 0.9435336 0.9400499 0.4338707 0.8540057
89 HOOK2 12876944 0.2273296 0.2503907 0.4380938 0.8540057
56 HOOK2 12877215 0.2742889 0.2915891 0.4528368 0.8551919
24 RNF39 30039208 0.1906980 0.2224265 0.4647508 0.8551919
98 GFPT2 179740992 0.6218308 0.5593665 0.4647508 0.8551919
120 FAM132A 1178202 0.7223557 0.7360413 0.4762820 0.8551919
154 UPK3B 76145589 0.2005878 0.2028450 0.4762820 0.8551919
22 RNF39 30039202 0.2191423 0.2489331 0.4806271 0.8551919
41 RNF39 30039303 0.1952517 0.2192596 0.4806271 0.8551919
91 HOOK2 12876937 0.2200042 0.2434971 0.4831279 0.8551919
26 RNF39 30039235 0.2208101 0.2505794 0.4967874 0.8662903
27 RNF39 30039239 0.3743278 0.4031679 0.5006483 0.8662903
40 RNF39 30039278 0.3615585 0.3906782 0.5299371 0.8977817
87 HOOK2 12876948 0.2284571 0.2494365 0.5305074 0.8977817
57 HOOK2 12877235 0.3353043 0.3606170 0.5467973 0.9123642
135 HLA-DPB1 33048542 0.0688653 0.0603714 0.5608346 0.9123642
123 FAM132A 1178172 0.8193061 0.8277238 0.5641490 0.9123642
38 RNF39 30039271 0.2125212 0.2314384 0.5687888 0.9123642
132 HLA-DPB1 33048423 0.9132301 0.9402103 0.5705938 0.9123642
82 HOOK2 12877020 0.2134993 0.2345430 0.5800855 0.9123642
143 IFI44L 79085647 0.1747650 0.1654684 0.5805954 0.9123642
42 RNF39 30039307 0.1771945 0.1703290 0.6135012 0.9283074
85 HOOK2 12876987 0.2178240 0.2403014 0.6142730 0.9283074
52 HOOK2 12877099 0.2162453 0.2355685 0.6316856 0.9283074
58 HOOK2 12877276 0.2293970 0.2577653 0.6316856 0.9283074
84 HOOK2 12876993 0.2123469 0.2326949 0.6316856 0.9283074
17 RNF39 30039127 0.3894824 0.3808942 0.6355221 0.9283074
59 BRDT 92414650 0.3600865 0.3375857 0.6355221 0.9283074
141 HLA-DPB1 33048592 0.9067151 0.9408180 0.6500147 0.9283074
61 BRDT 92414719 0.3011353 0.2798224 0.6539311 0.9283074
130 BRDT 92418017 0.9714090 0.9746152 0.6539311 0.9283074
53 HOOK2 12877107 0.2193410 0.2393899 0.6671087 0.9283074
92 HOOK2 12876926 0.2311439 0.2543572 0.6671087 0.9283074
148 UPK3B 76145702 0.3263160 0.3162807 0.6691047 0.9283074
83 HOOK2 12876997 0.2033761 0.2247642 0.6851025 0.9420160
88 HOOK2 12876946 0.2236624 0.2482356 0.7032727 0.9445535
90 HOOK2 12876942 0.2311652 0.2537722 0.7032727 0.9445535
142 HLA-DPB1 33048602 0.4550854 0.5601226 0.7053484 0.9445535
49 RNF39 30039415 0.2872570 0.2830408 0.7295468 0.9614919
16 RNF39 30039123 0.4496789 0.4621913 0.7488942 0.9614919
153 UPK3B 76145606 0.4234001 0.4142247 0.7488942 0.9614919
35 SMAD3 67361821 0.9322478 0.9362776 0.7502911 0.9614919
55 HOOK2 12877201 0.3137922 0.3270499 0.7587485 0.9614919
21 RNF39 30039186 0.2219051 0.2363932 0.7683973 0.9614919
122 FAM132A 1178182 0.7392234 0.7395861 0.7683973 0.9614919
54 HOOK2 12877138 0.2519799 0.2716501 0.7775298 0.9614919
147 UPK3B 76145717 0.4805704 0.4812723 0.7856472 0.9614919
131 HLA-DPB1 33048417 0.8982112 0.9160670 0.7875857 0.9614919
45 RNF39 30039349 0.2382702 0.2376113 0.7880446 0.9614919
126 FAM132A 1178136 0.9681518 0.9679960 0.8078245 0.9614919
93 HOOK2 12876918 0.2415910 0.2674003 0.8154662 0.9614919
44 RNF39 30039323 0.2900312 0.2873683 0.8277251 0.9614919
129 FAM132A 1178086 0.9048460 0.9001452 0.8277251 0.9614919
81 TLR1 38805839 0.0862660 0.0720627 0.8309871 0.9614919
149 UPK3B 76145693 0.5693504 0.5680260 0.8459705 0.9614919
125 FAM132A 1178150 0.9015033 0.9027851 0.8477344 0.9614919
48 RNF39 30039411 0.4398426 0.4386664 0.8561231 0.9614919
36 SMAD3 67361896 0.9011689 0.8989773 0.8610559 0.9614919
43 RNF39 30039313 0.2391492 0.2359025 0.8678401 0.9614919
46 RNF39 30039354 0.2384689 0.2416944 0.8678401 0.9614919
64 BRDT 92414793 0.5605071 0.5714565 0.8678401 0.9614919
150 UPK3B 76145689 0.4091882 0.4044889 0.8678401 0.9614919
94 HOOK2 12876911 0.2664089 0.2886766 0.8925354 0.9817889
60 BRDT 92414661 0.4353187 0.4161603 0.9082902 0.9821410
68 HELZ2 62199061 0.0389775 0.0418837 0.9095632 0.9821410
86 HOOK2 12876969 0.2223231 0.2438928 0.9119881 0.9821410
34 SMAD3 67361798 0.9436187 0.9337478 0.9365277 0.9874460
18 RNF39 30039130 0.2177503 0.2204855 0.9483698 0.9874460
50 RNF39 30039418 0.4424677 0.4368291 0.9489740 0.9874460
62 BRDT 92414751 0.5054684 0.5087828 0.9489740 0.9874460
124 FAM132A 1178162 0.7826432 0.7907324 0.9489740 0.9874460
39 RNF39 30039274 0.2189513 0.2283204 0.9690080 0.9952213
19 RNF39 30039132 0.1468104 0.1563233 0.9693714 0.9952213
139 HLA-DPB1 33048575 0.9091051 0.9340088 0.9773749 0.9967929
140 HLA-DPB1 33048581 0.8955914 0.9175717 0.9886847 1.0000000
63 BRDT 92414770 0.5120284 0.5148409 1.0000000 1.0000000
138 HLA-DPB1 33048571 0.9044165 0.9229893 1.0000000 1.0000000

3.4.4.2 Figure19: The Differential methylated CpGsites between dcSSc patients and lcSSc patients

[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 19 in our analysis."

3.5 PartII Summary:

Here, In Part II, we conducted the differential methylation analysis with the validation datasets, as we have confirmed its high correlation with the results of DNA methylation 450K. And in our analysis, we divided the CpGsites into two subgroups: The CpGsites shared in the two stages and the CpGsites only in the validaton stage. And we separately calculated and plotted its methylation status in different comparisons as well as in different cell types. We found that the genes such as MX1, EIF2AK2,IFI44L,PARP9 and IFITM1 are the main genes showing differential methylation between cases and controls in CD4+ and CD8+. And all these genes are belong to or associated with the type I interferon pathway, thus confirming and validating our previous GO analysis that the GO term like Type I interferon regulation is associated with SSc. Also, we found that the in the subgroup analysis, especially in dcSSc vs. Control, we can hardly find any significantly differential methylated sites, while in lcSSc vs. Control comparison, we found more significant CpGsites even than in the total SSc vs. Control comparison, indicating the consistency between the lcSSc patients, and also indicating the complexity between the methylation status of the dcSSc patients. Thus, our data suggested that, from the perspective of DNA methylation changes, the lcSSc patients are more consistent than the dcSSc patients, indicating the further exploration of the consistentcy and the uniqueness of the dcSSc epigenetic changes. In addition, we found that there are more significant CpGsites in CD8+ T cells than in the CD4+ T cells’ comparison, indicating the more severely epigenetic changes in CD8+ T cells, which need much more further exploration for its important role in SSc pathogenesis.

4 Part III: Differential gene expression in CD4+/CD8+ T cells and its correlation with gene methylation

4.1 Differential gene expression in CD4+ T cells between SSc patients and Controls

4.1.1 Table 22: The Differential expression between SSc patients and Controls

Genes Mean.Case Mean.Control Case.CI1 Case.CI2 Control.CI1 Control.CI2 P.value FDR
IFI44L 8.046350 1.273579 7.036447 9.056254 1.231390 1.315768 0.0198656 0.0331093
IFITM1 2.870440 1.147245 2.714960 3.025920 1.117331 1.177160 0.0056352 0.0140879
MX1 2.865622 1.185428 2.733170 2.998075 1.155190 1.215667 0.0296189 0.0370236
PARP9 6.659666 1.430793 6.336573 6.982759 1.381182 1.480404 0.0004580 0.0022900
EIF2AK2 1.992502 1.120276 1.853987 2.131017 1.064743 1.175809 0.1230055 0.1230055

4.1.2 Figure20: The Differential expression between SSc patients and Controls

[1] "Plot the Expression status of IFI44L"

[1] "Plot the Expression status of IFITM1"

[1] "Plot the Expression status of MX1"

[1] "Plot the Expression status of PARP9"

[1] "Plot the Expression status of EIF2AK2"

4.2 Differential gene expression in CD8+ T cells between SSc patients and Controls

4.2.1 Table 23: The Differential expression between SSc patients and Controls

Genes Mean.Case Mean.Control Case.CI1 Case.CI2 Control.CI1 Control.CI2 P.value FDR
IFI44L 4.395221 1.966491 4.055546 4.734896 1.845879 2.087103 0.0657267 0.0821583
IFITM1 1.636151 1.076445 1.588943 1.683359 1.059281 1.093609 0.0202463 0.0821583
MX1 3.112866 1.468340 2.952946 3.272786 1.408011 1.528668 0.0527902 0.0821583
PARP9 4.931086 1.227470 4.530545 5.331627 1.195379 1.259562 0.0596821 0.0821583
EIF2AK2 1.282878 1.211615 1.215745 1.350011 1.120513 1.302716 0.7393644 0.7393644

4.2.2 Figure21: The Differential expression between SSc patients and Controls

[1] "Plot the Expression status of IFI44L"

[1] "Plot the Expression status of IFITM1"

[1] "Plot the Expression status of MX1"

[1] "Plot the Expression status of PARP9"

[1] "Plot the Expression status of EIF2AK2"

4.3 Correlation between gene expression and methylation in CD4+ T cells

4.3.1 Table 24: The correlation between expression and methylation in CD4+ T cells

CpGs Gene Corr Corr.p Lm.r2
79085586 IFI44L -0.39 0.0316 0.1545703
79085765 IFI44L -0.34 0.0640 0.1172578
79085713 IFI44L -0.31 0.0930 0.0975002
79085647 IFI44L -0.24 0.1950 0.0593440
312463 IFITM1 0.23 0.2350 0.0537058
42798765 MX1 -0.20 0.2890 0.0386963
42798723 MX1 -0.19 0.3030 0.0364615
122281975 PARP9 -0.19 0.3050 0.0362413
42798747 MX1 -0.19 0.3070 0.0360014
42798698 MX1 -0.19 0.3190 0.0343050
42798749 MX1 -0.18 0.3430 0.0309958
42798857 MX1 -0.18 0.3450 0.0307559
122281939 PARP9 -0.15 0.4080 0.0237587
42798695 MX1 -0.14 0.4390 0.0207603
42798863 MX1 -0.14 0.4530 0.0195934
42798829 MX1 -0.13 0.4710 0.0181008
42798847 MX1 -0.13 0.4720 0.0179492
37383623 EIF2AK2 0.28 0.4720 0.0762774
42798818 MX1 -0.13 0.4750 0.0177674
42798816 MX1 -0.13 0.5010 0.0157895
42798837 MX1 -0.12 0.5070 0.0153241
37383588 EIF2AK2 -0.24 0.5340 0.0574691
42798733 MX1 -0.10 0.5890 0.0102004
42798781 MX1 -0.09 0.6350 0.0078751
312518 IFITM1 0.14 0.6380 0.0208792
313354 IFITM1 -0.09 0.6440 0.0074461
313408 IFITM1 -0.09 0.6470 0.0073308
37383713 EIF2AK2 0.14 0.7110 0.0208512
37383679 EIF2AK2 0.13 0.7400 0.0167979
42798813 MX1 -0.05 0.7910 0.0024505
37383730 EIF2AK2 -0.09 0.8150 0.0083731
37383568 EIF2AK2 0.09 0.8260 0.0073508
312419 IFITM1 -0.04 0.8400 0.0019811
312434 IFITM1 -0.01 0.9510 0.0001820

4.3.2 Figure22: The correlation between expression and methylation in CD4+ T cells

4.4 Correlation between gene expression and methylation in CD8+ T cells

4.4.1 Table 25: The correlation between expression and methylation in CD8+ T cells

CpGs Gene Corr Corr.p Lm.r2
79085586 IFI44L -0.37 0.0383 0.1353133
79085765 IFI44L -0.36 0.0446 0.1277101
79085647 IFI44L -0.33 0.0620 0.1112939
42798747 MX1 -0.28 0.1030 0.0784902
122281939 PARP9 -0.29 0.1030 0.0863589
79085713 IFI44L -0.29 0.1130 0.0816564
42798723 MX1 -0.26 0.1310 0.0678477
37383730 EIF2AK2 -0.55 0.1600 0.3004069
122281975 PARP9 -0.25 0.1700 0.0619500
42798698 MX1 -0.23 0.1760 0.0546541
312463 IFITM1 -0.26 0.1850 0.0691613
42798781 MX1 -0.21 0.2360 0.0423371
42798695 MX1 -0.17 0.3250 0.0293229
312434 IFITM1 -0.19 0.3710 0.0349896
37383568 EIF2AK2 0.34 0.4130 0.1143366
42798863 MX1 -0.13 0.4500 0.0173745
42798813 MX1 -0.13 0.4530 0.0171822
312419 IFITM1 -0.15 0.4700 0.0229366
42798837 MX1 -0.12 0.4800 0.0151987
42798829 MX1 -0.12 0.4850 0.0149143
42798765 MX1 -0.12 0.4890 0.0145876
42798857 MX1 -0.11 0.5310 0.0119887
37383713 EIF2AK2 -0.26 0.5310 0.0686151
42798816 MX1 -0.11 0.5390 0.0115668
42798847 MX1 -0.11 0.5440 0.0112528
37383588 EIF2AK2 0.25 0.5500 0.0626145
37383623 EIF2AK2 0.23 0.5800 0.0540205
42798818 MX1 -0.09 0.5880 0.0089814
42798733 MX1 -0.09 0.6230 0.0074243
313408 IFITM1 -0.08 0.6540 0.0061667
42798749 MX1 -0.07 0.6700 0.0055590
312518 IFITM1 -0.10 0.7200 0.0094701
313354 IFITM1 0.05 0.7580 0.0029280
37383679 EIF2AK2 -0.05 0.9080 0.0024280

4.4.2 Figure23: The correlation between expression and methylation in CD8+ T cells

4.5 Correlation between gene expression and methylation in CD4+ and CD8+ T cells

4.5.1 Table26: The correlation between expression and methylation in CD4+ and CD8+ T cells

CpGs Gene Corr Corr.p Lm.r2
79085586 IFI44L -0.32 0.0114 0.1018940
79085765 IFI44L -0.28 0.0257 0.0802068
79085713 IFI44L -0.27 0.0353 0.0717273
122281975 PARP9 -0.24 0.0602 0.0566870
122281939 PARP9 -0.24 0.0635 0.0553203
42798747 MX1 -0.23 0.0656 0.0519690
79085647 IFI44L -0.23 0.0782 0.0508008
42798723 MX1 -0.21 0.0893 0.0444426
42798698 MX1 -0.18 0.1440 0.0330772
42798781 MX1 -0.14 0.2670 0.0191954
42798695 MX1 -0.14 0.2710 0.0188882
312463 IFITM1 0.13 0.3350 0.0175711
37383588 EIF2AK2 -0.24 0.3440 0.0598388
42798863 MX1 -0.11 0.3830 0.0119045
312419 IFITM1 -0.12 0.4110 0.0147693
42798857 MX1 -0.10 0.4120 0.0105492
42798765 MX1 -0.10 0.4170 0.0103252
42798829 MX1 -0.09 0.4480 0.0090064
42798837 MX1 -0.09 0.4690 0.0082269
42798816 MX1 -0.09 0.4780 0.0078791
42798813 MX1 -0.08 0.5140 0.0066742
42798847 MX1 -0.08 0.5140 0.0066985
42798749 MX1 -0.08 0.5460 0.0057101
42798818 MX1 -0.07 0.5680 0.0051275
42798733 MX1 -0.07 0.5760 0.0049210
37383713 EIF2AK2 0.12 0.6440 0.0145916
37383679 EIF2AK2 0.10 0.7090 0.0095426
312434 IFITM1 -0.05 0.7520 0.0021864
37383623 EIF2AK2 -0.08 0.7550 0.0066994
312518 IFITM1 0.05 0.7970 0.0024817
313408 IFITM1 0.03 0.8080 0.0009252
37383568 EIF2AK2 0.06 0.8100 0.0039840
37383730 EIF2AK2 -0.06 0.8270 0.0033006
313354 IFITM1 0.00 0.9970 0.0000002

4.5.2 Figure24: The correlation between expression and methylation in CD4+ and CD8+ T cells

4.6 PartIII Summary:

In this part, we conducted the differential expression analysis between the SSc patients and Controls in both CD4+ and CD8+ T cells. And we found that nearly all of the genes showing differential methylation status in CD4+ and CD8+ T cells. However, due to the limited sample sizes, we found some of them showed marginal p-value which needs further confirmation with larger sample size. And In the correlation analysis between DNA methylation and expression, we only found the IFI44L gene showing significant negative correlation between methylation and expression. And we also found the other genes also showing negative correlation though the p-value of the correlation is not significant. And we believe that the limited sample sizes may be the main cause of it and further experiments are needed for convince it. In conclusion, with the above datasets, we still believe that the methylation and expression changes in the type I IFN related genes were negative and consistent, and the decreased methylation in SSc patients leads to the higher expression of these genes in CD4+ and CD8+ T cells, thus may induce further biological changes and might be associated with SSc pathogenesis.

5 Part IV: Differential serum type I IFN level and its correlation with gene expression and methylation

5.1 Figure 25: Differential serum type I IFN alpha level between SSc patients and Controls

[1] "The Mean Type I IFN alpha level in SSc is 25.174362, and The Mean Type I IFN alpha level in Control is 14.424465, the p-value between cases and controls conducted with wilcox signed rank test is 0.00000064"
[1] "Plot the Expression status of type I IFN alpha"

5.2 Figure 26: Differential serum type I IFN beta level between SSc patients and Controls

[1] "The Mean Type I IFN beta level in SSc is 91.090179, and The Mean Type I IFN beta level in Control is 40.276884, the p-value between cases and controls conducted with wilcox signed rank test is 0.00203729"
[1] "Plot the Expression status of type I IFN beta"

5.3 Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells

5.3.1 Table 27: Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells

Genes Corr Corr.p Lm.r2
IFITM1 0.32 0.0315 0.1054195
IFI44L 0.30 0.0518 0.0870987
PARP9 0.23 0.1380 0.0515756
MX1 0.13 0.4130 0.0160291
EIF2AK2 0.19 0.4230 0.0359393

5.3.2 Figure27: Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells

5.4 Correlation of serum type I IFN beta level and gene expression in CD4+ T cells

5.4.1 Table 28: Correlation of serum type I IFN beta level and gene expression in CD4+ T cells

Genes Corr Corr.p Lm.r2
IFITM1 0.46 0.00165 0.2121877
EIF2AK2 0.61 0.00452 0.3687833
PARP9 0.42 0.00497 0.1731270
MX1 0.25 0.09790 0.0638792
IFI44L 0.10 0.50000 0.0109112

5.4.2 Figure28: Correlation of serum type I IFN beta level and gene expression in CD4+ T cells

5.5 Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells

5.5.1 Table 29: Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells

Genes Corr Corr.p Lm.r2
EIF2AK2 -0.41 0.0690 0.1720944
IFI44L 0.26 0.0804 0.0693922
MX1 0.25 0.0924 0.0644428
IFITM1 0.17 0.2660 0.0287167
PARP9 0.07 0.6680 0.0043210

5.5.2 Figure29: Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells

5.6 Correlation of serum type I IFN beta level and gene expression in CD8+ T cells

5.6.1 Table 30: Correlation of serum type I IFN beta level and gene expression in CD8+ T cells

Genes Corr Corr.p Lm.r2
IFITM1 0.24 0.106 0.0596911
PARP9 0.19 0.201 0.0377456
MX1 0.19 0.206 0.0368811
IFI44L 0.06 0.707 0.0033088
EIF2AK2 0.07 0.773 0.0047385

5.6.2 Figure30: Correlation of serum type I IFN beta level and gene expression in CD8+ T cells

5.7 Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells

5.7.1 Table 31:Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells

CpGs CpGnames Gene Corr.alpha P.value FDR
112 62199181 cg06064964 HELZ2 0.45 0.000429 0.0701575
84 313354 cg11694510 IFITM1 -0.41 0.000665 0.0701575
104 122281975 cg00959259 PARP9 -0.38 0.002060 0.1448867
103 122281939 cg08122652 PARP9 -0.33 0.008120 0.4283300
114 37383568 cg17326313 EIF2AK2 -0.31 0.012800 0.5244857
208 79085713 cg17980508 IFI44L -0.30 0.015600 0.5244857
206 79085586 cg03607951 IFI44L -0.30 0.017400 0.5244857
16 42798863 Not In Discovery MX1 -0.26 0.039500 0.8419314
15 42798857 Not In Discovery MX1 -0.26 0.040200 0.8419314
14 42798847 Not In Discovery MX1 -0.25 0.044300 0.8419314
12 42798829 Not In Discovery MX1 -0.25 0.047400 0.8419314
10 42798816 Not In Discovery MX1 -0.24 0.052100 0.8419314
115 37383588 Not In Discovery EIF2AK2 -0.24 0.052100 0.8419314
207 79085647 Not In Discovery IFI44L -0.24 0.059100 0.8419314
209 79085765 cg00855901 IFI44L -0.23 0.064300 0.8419314
5 42798747 cg08924203 MX1 -0.23 0.069800 0.8419314
3 42798723 Not In Discovery MX1 -0.22 0.075700 0.8419314
85 313408 Not In Discovery IFITM1 -0.22 0.077700 0.8419314
180 1178105 Not In Discovery FAM132A -0.22 0.079300 0.8419314
49 76145702 Not In Discovery UPK3B -0.21 0.091100 0.8419314
13 42798837 Not In Discovery MX1 -0.21 0.092800 0.8419314
22 67361798 Not In Discovery SMAD3 0.21 0.095700 0.8419314
57 76145589 Not In Discovery UPK3B 0.20 0.103000 0.8419314
95 92414661 Not In Discovery BRDT -0.20 0.108000 0.8419314
178 1178136 Not In Discovery FAM132A -0.20 0.115000 0.8419314
2 42798698 Not In Discovery MX1 -0.20 0.117000 0.8419314
100 92414770 Not In Discovery BRDT -0.20 0.119000 0.8419314
185 33048423 Not In Discovery HLA-DPB1 -0.20 0.123000 0.8419314
97 92414722 cg14732540 BRDT -0.19 0.129000 0.8419314
130 38805839 Not In Discovery TLR1 -0.20 0.129000 0.8419314
11 42798818 Not In Discovery MX1 -0.19 0.131000 0.8419314
184 33048417 Not In Discovery HLA-DPB1 -0.19 0.134000 0.8419314
101 92414782 cg02935097 BRDT -0.19 0.135000 0.8419314
110 62199061 Not In Discovery HELZ2 0.20 0.138000 0.8419314
6 42798749 Not In Discovery MX1 -0.18 0.153000 0.8419314
188 33048469 cg10850215 HLA-DPB1 -0.18 0.162000 0.8419314
9 42798813 Not In Discovery MX1 -0.17 0.164000 0.8419314
186 33048433 Not In Discovery HLA-DPB1 -0.18 0.169000 0.8419314
21 67361773 cg24961286 SMAD3 0.17 0.177000 0.8419314
197 33048555 cg19990651 HLA-DPB1 -0.17 0.181000 0.8419314
99 92414751 Not In Discovery BRDT -0.17 0.190000 0.8419314
177 1178150 Not In Discovery FAM132A -0.17 0.190000 0.8419314
191 33048502 cg26645432 HLA-DPB1 -0.17 0.193000 0.8419314
199 33048571 Not In Discovery HLA-DPB1 -0.16 0.202000 0.8419314
203 33048602 Not In Discovery HLA-DPB1 -0.16 0.202000 0.8419314
102 92414793 Not In Discovery BRDT -0.16 0.210000 0.8419314
113 62199190 cg09844573 HELZ2 0.17 0.212000 0.8419314
111 62199156 cg11779113 HELZ2 0.17 0.218000 0.8419314
23 67361821 Not In Discovery SMAD3 0.16 0.219000 0.8419314
176 1178162 Not In Discovery FAM132A -0.16 0.219000 0.8419314
1 42798695 Not In Discovery MX1 -0.15 0.227000 0.8419314
174 1178182 Not In Discovery FAM132A -0.15 0.230000 0.8419314
44 30039208 Not In Discovery RNF39 0.15 0.236000 0.8419314
19 33048310 cg13349035 HLA-DPB1 -0.15 0.249000 0.8419314
198 33048558 cg01132696 HLA-DPB1 -0.15 0.251000 0.8419314
202 33048592 Not In Discovery HLA-DPB1 -0.14 0.261000 0.8419314
200 33048575 Not In Discovery HLA-DPB1 -0.14 0.262000 0.8419314
42 30039202 Not In Discovery RNF39 0.14 0.269000 0.8419314
51 76145689 Not In Discovery UPK3B -0.14 0.271000 0.8419314
187 33048444 Not In Discovery HLA-DPB1 -0.14 0.278000 0.8419314
17 33048286 cg09234582 HLA-DPB1 -0.14 0.285000 0.8419314
18 33048291 cg25045942 HLA-DPB1 -0.13 0.296000 0.8419314
190 33048485 cg17588455 HLA-DPB1 -0.13 0.297000 0.8419314
118 37383713 Not In Discovery EIF2AK2 -0.13 0.301000 0.8419314
193 33048540 cg14870156 HLA-DPB1 -0.13 0.303000 0.8419314
195 33048544 Not In Discovery HLA-DPB1 -0.13 0.310000 0.8419314
196 33048549 Not In Discovery HLA-DPB1 -0.13 0.310000 0.8419314
98 92414737 cg13299824 BRDT -0.13 0.311000 0.8419314
201 33048581 Not In Discovery HLA-DPB1 -0.13 0.320000 0.8419314
183 92418017 Not In Discovery BRDT -0.12 0.325000 0.8419314
37 30039142 cg00947782 RNF39 0.12 0.334000 0.8419314
8 42798781 Not In Discovery MX1 -0.12 0.344000 0.8419314
205 312463 Not In Discovery IFITM1 -0.13 0.347000 0.8419314
96 92414719 Not In Discovery BRDT -0.12 0.351000 0.8419314
92 12877235 Not In Discovery HOOK2 -0.12 0.357000 0.8419314
131 12877020 Not In Discovery HOOK2 -0.12 0.358000 0.8419314
144 12876911 Not In Discovery HOOK2 -0.12 0.361000 0.8419314
132 12877001 cg11738485 HOOK2 -0.12 0.362000 0.8419314
135 12876987 Not In Discovery HOOK2 -0.12 0.362000 0.8419314
140 12876942 Not In Discovery HOOK2 -0.11 0.362000 0.8419314
139 12876944 Not In Discovery HOOK2 -0.11 0.363000 0.8419314
143 12876918 Not In Discovery HOOK2 -0.11 0.365000 0.8419314
43 30039206 Not In Discovery RNF39 0.11 0.366000 0.8419314
93 12877276 Not In Discovery HOOK2 -0.11 0.366000 0.8419314
137 12876948 Not In Discovery HOOK2 -0.11 0.367000 0.8419314
138 12876946 Not In Discovery HOOK2 -0.11 0.371000 0.8419314
192 33048529 cg06437840 HLA-DPB1 -0.11 0.372000 0.8419314
91 12877215 Not In Discovery HOOK2 -0.11 0.374000 0.8419314
134 12876993 Not In Discovery HOOK2 -0.11 0.375000 0.8419314
142 12876926 Not In Discovery HOOK2 -0.11 0.375000 0.8419314
88 12877138 Not In Discovery HOOK2 -0.11 0.376000 0.8419314
136 12876969 Not In Discovery HOOK2 -0.11 0.376000 0.8419314
179 1178118 Not In Discovery FAM132A 0.11 0.376000 0.8419314
141 12876937 Not In Discovery HOOK2 -0.11 0.377000 0.8419314
133 12876997 Not In Discovery HOOK2 -0.11 0.383000 0.8419314
106 75954053 cg25716013 COX7A2 -0.11 0.390000 0.8419314
86 12877099 Not In Discovery HOOK2 -0.11 0.393000 0.8419314
39 30039158 Not In Discovery RNF39 0.11 0.394000 0.8419314
56 76145606 Not In Discovery UPK3B 0.11 0.402000 0.8419314
87 12877107 Not In Discovery HOOK2 -0.11 0.404000 0.8419314
211 312518 cg05432003 IFITM1 -0.17 0.405000 0.8419314
90 12877201 Not In Discovery HOOK2 -0.10 0.407000 0.8419314
189 33048483 cg03229061 HLA-DPB1 -0.10 0.423000 0.8665340
46 30039235 Not In Discovery RNF39 0.10 0.443000 0.8987788
94 92414650 Not In Discovery BRDT -0.10 0.453000 0.9103143
89 12877188 cg23899408 HOOK2 -0.09 0.458000 0.9116792
83 21572623 cg12639429 TTC39C -0.09 0.464000 0.9149907
82 21572635 cg05401069 TTC39C -0.09 0.469000 0.9162870
4 42798733 Not In Discovery MX1 -0.09 0.482000 0.9284000
41 30039186 Not In Discovery RNF39 0.09 0.484000 0.9284000
182 92417998 cg01081438 BRDT 0.08 0.510000 0.9393313
28 75953883 Not In Discovery COX7A2 -0.08 0.512000 0.9393313
45 30039232 Not In Discovery RNF39 0.08 0.531000 0.9393313
204 312434 Not In Discovery IFITM1 -0.09 0.540000 0.9393313
123 179741081 Not In Discovery GFPT2 0.08 0.553000 0.9393313
122 179741101 Not In Discovery GFPT2 0.07 0.582000 0.9393313
128 179741039 Not In Discovery GFPT2 0.07 0.586000 0.9393313
149 179740970 Not In Discovery GFPT2 0.07 0.590000 0.9393313
127 179741042 Not In Discovery GFPT2 0.07 0.591000 0.9393313
79 30039466 cg16078649 RNF39 -0.07 0.598000 0.9393313
31 75953960 Not In Discovery COX7A2 -0.07 0.603000 0.9393313
175 1178172 Not In Discovery FAM132A -0.07 0.603000 0.9393313
73 30039411 Not In Discovery RNF39 0.07 0.609000 0.9393313
54 76145628 Not In Discovery UPK3B -0.06 0.614000 0.9393313
36 30039132 Not In Discovery RNF39 0.06 0.616000 0.9393313
76 30039432 cg13401893 RNF39 -0.06 0.619000 0.9393313
105 75954022 Not In Discovery COX7A2 -0.06 0.620000 0.9393313
124 179741067 Not In Discovery GFPT2 0.06 0.621000 0.9393313
32 75953974 Not In Discovery COX7A2 -0.06 0.622000 0.9393313
147 179740994 Not In Discovery GFPT2 0.06 0.624000 0.9393313
150 179740963 Not In Discovery GFPT2 0.06 0.629000 0.9393313
155 179740920 Not In Discovery GFPT2 0.06 0.630000 0.9393313
159 179740900 Not In Discovery GFPT2 0.06 0.630000 0.9393313
153 179740940 Not In Discovery GFPT2 0.06 0.635000 0.9393313
126 179741060 Not In Discovery GFPT2 0.06 0.636000 0.9393313
30 75953937 Not In Discovery COX7A2 -0.06 0.640000 0.9393313
151 179740957 Not In Discovery GFPT2 0.06 0.647000 0.9393313
154 179740935 Not In Discovery GFPT2 0.06 0.648000 0.9393313
152 179740955 Not In Discovery GFPT2 0.06 0.650000 0.9393313
156 179740918 Not In Discovery GFPT2 0.06 0.651000 0.9393313
146 179740999 Not In Discovery GFPT2 0.06 0.657000 0.9393313
40 30039175 cg03343571 RNF39 0.06 0.661000 0.9393313
158 179740906 Not In Discovery GFPT2 0.06 0.662000 0.9393313
145 179741008 Not In Discovery GFPT2 0.05 0.663000 0.9393313
117 37383679 Not In Discovery EIF2AK2 0.05 0.666000 0.9393313
125 179741063 Not In Discovery GFPT2 0.05 0.669000 0.9393313
148 179740992 Not In Discovery GFPT2 0.05 0.669000 0.9393313
38 30039151 cg18930910 RNF39 0.05 0.680000 0.9393313
157 179740915 cg13944838 GFPT2 0.05 0.682000 0.9393313
48 76145717 Not In Discovery UPK3B -0.05 0.688000 0.9393313
160 179740888 Not In Discovery GFPT2 0.05 0.688000 0.9393313
58 30039271 Not In Discovery RNF39 -0.05 0.693000 0.9393313
121 179741105 cg23248424 GFPT2 0.05 0.693000 0.9393313
129 38805732 cg02016764 TLR1 0.05 0.693000 0.9393313
52 76145673 cg05372444 UPK3B -0.05 0.695000 0.9393313
66 30039354 Not In Discovery RNF39 -0.05 0.703000 0.9393313
116 37383623 Not In Discovery EIF2AK2 0.05 0.704000 0.9393313
107 75954118 Not In Discovery COX7A2 -0.05 0.710000 0.9393313
68 30039374 cg20249327 RNF39 -0.05 0.717000 0.9393313
20 33048370 Not In Discovery HLA-DPB1 -0.05 0.721000 0.9393313
108 75954122 Not In Discovery COX7A2 -0.05 0.724000 0.9393313
210 312419 Not In Discovery IFITM1 0.05 0.727000 0.9393313
75 30039418 Not In Discovery RNF39 -0.04 0.728000 0.9393313
120 179741121 cg02891314 GFPT2 0.04 0.733000 0.9393313
35 30039130 Not In Discovery RNF39 -0.04 0.738000 0.9393313
69 30039376 cg15877520 RNF39 -0.04 0.739000 0.9393313
109 62199034 cg17593958 HELZ2 0.04 0.748000 0.9429742
63 30039313 Not In Discovery RNF39 -0.04 0.758000 0.9429742
78 30039442 cg10568066 RNF39 -0.04 0.762000 0.9429742
7 42798765 Not In Discovery MX1 -0.04 0.779000 0.9429742
172 1178202 Not In Discovery FAM132A -0.04 0.779000 0.9429742
33 30039123 Not In Discovery RNF39 0.03 0.790000 0.9429742
119 37383730 Not In Discovery EIF2AK2 -0.03 0.792000 0.9429742
81 21572657 cg18719665 TTC39C -0.03 0.795000 0.9429742
166 179740840 Not In Discovery GFPT2 0.03 0.796000 0.9429742
71 30039403 cg09279736 RNF39 -0.03 0.799000 0.9429742
168 179740825 Not In Discovery GFPT2 0.03 0.799000 0.9429742
26 75953829 Not In Discovery COX7A2 -0.03 0.802000 0.9429742
161 179740869 Not In Discovery GFPT2 0.03 0.803000 0.9429742
24 67361896 Not In Discovery SMAD3 0.03 0.807000 0.9429742
62 30039307 Not In Discovery RNF39 -0.03 0.811000 0.9429742
47 30039239 Not In Discovery RNF39 0.03 0.814000 0.9429742
163 179740861 Not In Discovery GFPT2 0.03 0.818000 0.9429742
25 75953821 Not In Discovery COX7A2 0.03 0.824000 0.9429742
162 179740867 Not In Discovery GFPT2 0.03 0.832000 0.9429742
53 76145633 cg16453056 UPK3B -0.03 0.836000 0.9429742
164 179740855 Not In Discovery GFPT2 0.03 0.843000 0.9429742
165 179740852 Not In Discovery GFPT2 0.02 0.847000 0.9429742
167 179740832 Not In Discovery GFPT2 0.02 0.851000 0.9429742
29 75953935 cg19367436 COX7A2 -0.02 0.853000 0.9429742
61 30039303 Not In Discovery RNF39 -0.02 0.860000 0.9429742
50 76145693 Not In Discovery UPK3B -0.02 0.863000 0.9429742
169 179740822 Not In Discovery GFPT2 0.02 0.863000 0.9429742
64 30039323 Not In Discovery RNF39 -0.02 0.867000 0.9429742
72 30039408 cg07382347 RNF39 -0.02 0.876000 0.9478769
55 76145620 Not In Discovery UPK3B -0.02 0.891000 0.9526970
27 75953853 cg06809298 COX7A2 -0.02 0.894000 0.9526970
70 30039380 cg13918754 RNF39 -0.02 0.894000 0.9526970
60 30039278 Not In Discovery RNF39 0.01 0.924000 0.9790400
59 30039274 Not In Discovery RNF39 -0.01 0.928000 0.9790400
74 30039415 Not In Discovery RNF39 -0.01 0.938000 0.9819615
77 30039435 cg12633154 RNF39 0.01 0.951000 0.9819615
34 30039127 Not In Discovery RNF39 0.01 0.953000 0.9819615
171 1178207 Not In Discovery FAM132A -0.01 0.953000 0.9819615
65 30039349 Not In Discovery RNF39 -0.01 0.962000 0.9819615
67 30039364 Not In Discovery RNF39 0.01 0.964000 0.9819615
170 1178246 cg24345856 FAM132A 0.01 0.967000 0.9819615
181 1178086 Not In Discovery FAM132A -0.01 0.968000 0.9819615
80 30039476 cg10930308 RNF39 0.00 0.974000 0.9833206
173 1178192 Not In Discovery FAM132A 0.00 0.992000 0.9967238
194 33048542 Not In Discovery HLA-DPB1 0.00 0.999000 0.9990000

5.7.2 Figure31:Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells

##Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells

5.7.3 Table 32:Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells

CpGs CpGnames Gene Corr.beta P.value FDR
85 313408 Not In Discovery IFITM1 -0.40 0.000997 0.1696440
81 21572657 cg18719665 TTC39C 0.38 0.002020 0.1696440
109 62199034 cg17593958 HELZ2 0.40 0.002530 0.1696440
112 62199181 cg06064964 HELZ2 0.38 0.003710 0.1696440
82 21572635 cg05401069 TTC39C 0.35 0.004020 0.1696440
83 21572623 cg12639429 TTC39C 0.34 0.006060 0.1923114
115 37383588 Not In Discovery EIF2AK2 -0.34 0.006380 0.1923114
110 62199061 Not In Discovery HELZ2 0.32 0.015500 0.4032444
47 30039239 Not In Discovery RNF39 0.30 0.017200 0.4032444
51 76145689 Not In Discovery UPK3B -0.28 0.025900 0.5275000
84 313354 cg11694510 IFITM1 -0.28 0.027500 0.5275000
104 122281975 cg00959259 PARP9 -0.25 0.047200 0.7884737
43 30039206 Not In Discovery RNF39 0.25 0.050800 0.7884737
103 122281939 cg08122652 PARP9 -0.24 0.055900 0.7884737
52 76145673 cg05372444 UPK3B -0.23 0.062100 0.7884737
113 62199190 cg09844573 HELZ2 0.25 0.063500 0.7884737
114 37383568 cg17326313 EIF2AK2 -0.23 0.066700 0.7884737
27 75953853 cg06809298 COX7A2 -0.22 0.080600 0.7884737
25 75953821 Not In Discovery COX7A2 -0.22 0.083200 0.7884737
42 30039202 Not In Discovery RNF39 0.22 0.087400 0.7884737
15 42798857 Not In Discovery MX1 -0.21 0.091800 0.7884737
22 67361798 Not In Discovery SMAD3 0.21 0.097800 0.7884737
32 75953974 Not In Discovery COX7A2 -0.21 0.099100 0.7884737
16 42798863 Not In Discovery MX1 -0.21 0.100000 0.7884737
41 30039186 Not In Discovery RNF39 0.21 0.101000 0.7884737
46 30039235 Not In Discovery RNF39 0.21 0.103000 0.7884737
12 42798829 Not In Discovery MX1 -0.20 0.105000 0.7884737
28 75953883 Not In Discovery COX7A2 -0.21 0.109000 0.7884737
67 30039364 Not In Discovery RNF39 0.20 0.114000 0.7884737
173 1178192 Not In Discovery FAM132A -0.20 0.122000 0.7884737
182 92417998 cg01081438 BRDT 0.19 0.122000 0.7884737
35 30039130 Not In Discovery RNF39 0.19 0.132000 0.7884737
40 30039175 cg03343571 RNF39 0.19 0.133000 0.7884737
203 33048602 Not In Discovery HLA-DPB1 -0.19 0.133000 0.7884737
26 75953829 Not In Discovery COX7A2 -0.19 0.135000 0.7884737
45 30039232 Not In Discovery RNF39 0.19 0.138000 0.7884737
33 30039123 Not In Discovery RNF39 0.19 0.140000 0.7884737
206 79085586 cg03607951 IFI44L -0.19 0.142000 0.7884737
50 76145693 Not In Discovery UPK3B -0.18 0.147000 0.7953077
14 42798847 Not In Discovery MX1 -0.17 0.170000 0.8267755
3 42798723 Not In Discovery MX1 -0.17 0.172000 0.8267755
21 67361773 cg24961286 SMAD3 0.17 0.176000 0.8267755
31 75953960 Not In Discovery COX7A2 -0.17 0.191000 0.8267755
30 75953937 Not In Discovery COX7A2 -0.16 0.203000 0.8267755
19 33048310 cg13349035 HLA-DPB1 -0.16 0.206000 0.8267755
20 33048370 Not In Discovery HLA-DPB1 -0.16 0.212000 0.8267755
106 75954053 cg25716013 COX7A2 -0.16 0.212000 0.8267755
34 30039127 Not In Discovery RNF39 0.16 0.213000 0.8267755
11 42798818 Not In Discovery MX1 -0.15 0.225000 0.8267755
208 79085713 cg17980508 IFI44L -0.15 0.232000 0.8267755
170 1178246 cg24345856 FAM132A 0.15 0.238000 0.8267755
130 38805839 Not In Discovery TLR1 -0.15 0.249000 0.8267755
29 75953935 cg19367436 COX7A2 -0.15 0.251000 0.8267755
10 42798816 Not In Discovery MX1 -0.14 0.256000 0.8267755
105 75954022 Not In Discovery COX7A2 -0.14 0.259000 0.8267755
119 37383730 Not In Discovery EIF2AK2 -0.14 0.268000 0.8267755
9 42798813 Not In Discovery MX1 -0.14 0.271000 0.8267755
156 179740918 Not In Discovery GFPT2 -0.14 0.272000 0.8267755
44 30039208 Not In Discovery RNF39 0.14 0.277000 0.8267755
13 42798837 Not In Discovery MX1 -0.14 0.278000 0.8267755
17 33048286 cg09234582 HLA-DPB1 -0.14 0.281000 0.8267755
155 179740920 Not In Discovery GFPT2 -0.14 0.281000 0.8267755
169 179740822 Not In Discovery GFPT2 -0.14 0.281000 0.8267755
160 179740888 Not In Discovery GFPT2 -0.13 0.293000 0.8267755
23 67361821 Not In Discovery SMAD3 0.13 0.296000 0.8267755
100 92414770 Not In Discovery BRDT -0.13 0.307000 0.8267755
162 179740867 Not In Discovery GFPT2 -0.13 0.309000 0.8267755
145 179741008 Not In Discovery GFPT2 -0.13 0.311000 0.8267755
194 33048542 Not In Discovery HLA-DPB1 0.13 0.312000 0.8267755
175 1178172 Not In Discovery FAM132A -0.13 0.314000 0.8267755
157 179740915 cg13944838 GFPT2 -0.13 0.318000 0.8267755
7 42798765 Not In Discovery MX1 -0.12 0.326000 0.8267755
158 179740906 Not In Discovery GFPT2 -0.12 0.327000 0.8267755
57 76145589 Not In Discovery UPK3B 0.12 0.328000 0.8267755
128 179741039 Not In Discovery GFPT2 -0.12 0.331000 0.8267755
151 179740957 Not In Discovery GFPT2 -0.12 0.332000 0.8267755
172 1178202 Not In Discovery FAM132A -0.12 0.332000 0.8267755
107 75954118 Not In Discovery COX7A2 -0.12 0.339000 0.8267755
102 92414793 Not In Discovery BRDT -0.12 0.341000 0.8267755
154 179740935 Not In Discovery GFPT2 -0.12 0.343000 0.8267755
149 179740970 Not In Discovery GFPT2 -0.12 0.345000 0.8267755
181 1178086 Not In Discovery FAM132A -0.12 0.346000 0.8267755
1 42798695 Not In Discovery MX1 -0.12 0.352000 0.8267755
5 42798747 cg08924203 MX1 -0.12 0.352000 0.8267755
153 179740940 Not In Discovery GFPT2 -0.12 0.354000 0.8267755
146 179740999 Not In Discovery GFPT2 -0.12 0.355000 0.8267755
159 179740900 Not In Discovery GFPT2 -0.12 0.361000 0.8267755
152 179740955 Not In Discovery GFPT2 -0.11 0.362000 0.8267755
127 179741042 Not In Discovery GFPT2 -0.11 0.369000 0.8267755
165 179740852 Not In Discovery GFPT2 -0.11 0.370000 0.8267755
147 179740994 Not In Discovery GFPT2 -0.11 0.374000 0.8267755
167 179740832 Not In Discovery GFPT2 -0.11 0.375000 0.8267755
108 75954122 Not In Discovery COX7A2 -0.11 0.376000 0.8267755
210 312419 Not In Discovery IFITM1 -0.13 0.378000 0.8267755
111 62199156 cg11779113 HELZ2 0.12 0.380000 0.8267755
148 179740992 Not In Discovery GFPT2 -0.11 0.382000 0.8267755
150 179740963 Not In Discovery GFPT2 -0.11 0.384000 0.8267755
163 179740861 Not In Discovery GFPT2 -0.11 0.384000 0.8267755
18 33048291 cg25045942 HLA-DPB1 -0.11 0.391000 0.8293762
166 179740840 Not In Discovery GFPT2 -0.11 0.396000 0.8293762
204 312434 Not In Discovery IFITM1 -0.13 0.397000 0.8293762
56 76145606 Not In Discovery UPK3B -0.10 0.409000 0.8379135
171 1178207 Not In Discovery FAM132A -0.10 0.410000 0.8379135
126 179741060 Not In Discovery GFPT2 -0.10 0.413000 0.8379135
125 179741063 Not In Discovery GFPT2 -0.10 0.419000 0.8415030
168 179740825 Not In Discovery GFPT2 -0.10 0.424000 0.8415030
124 179741067 Not In Discovery GFPT2 -0.10 0.430000 0.8415030
123 179741081 Not In Discovery GFPT2 -0.10 0.438000 0.8415030
164 179740855 Not In Discovery GFPT2 -0.10 0.441000 0.8415030
161 179740869 Not In Discovery GFPT2 -0.09 0.461000 0.8415030
6 42798749 Not In Discovery MX1 -0.09 0.468000 0.8415030
120 179741121 cg02891314 GFPT2 -0.09 0.478000 0.8415030
39 30039158 Not In Discovery RNF39 0.09 0.486000 0.8415030
187 33048444 Not In Discovery HLA-DPB1 -0.09 0.492000 0.8415030
8 42798781 Not In Discovery MX1 -0.09 0.496000 0.8415030
121 179741105 cg23248424 GFPT2 -0.09 0.504000 0.8415030
53 76145633 cg16453056 UPK3B -0.08 0.512000 0.8415030
48 76145717 Not In Discovery UPK3B -0.08 0.524000 0.8415030
122 179741101 Not In Discovery GFPT2 -0.08 0.525000 0.8415030
198 33048558 cg01132696 HLA-DPB1 -0.08 0.531000 0.8415030
117 37383679 Not In Discovery EIF2AK2 0.08 0.538000 0.8415030
72 30039408 cg07382347 RNF39 -0.08 0.539000 0.8415030
202 33048592 Not In Discovery HLA-DPB1 -0.08 0.540000 0.8415030
205 312463 Not In Discovery IFITM1 -0.08 0.540000 0.8415030
207 79085647 Not In Discovery IFI44L 0.08 0.544000 0.8415030
101 92414782 cg02935097 BRDT -0.08 0.554000 0.8415030
180 1178105 Not In Discovery FAM132A -0.07 0.556000 0.8415030
68 30039374 cg20249327 RNF39 -0.07 0.557000 0.8415030
131 12877020 Not In Discovery HOOK2 -0.07 0.568000 0.8415030
211 312518 cg05432003 IFITM1 -0.12 0.574000 0.8415030
58 30039271 Not In Discovery RNF39 -0.07 0.583000 0.8415030
199 33048571 Not In Discovery HLA-DPB1 -0.07 0.583000 0.8415030
133 12876997 Not In Discovery HOOK2 -0.07 0.589000 0.8415030
135 12876987 Not In Discovery HOOK2 -0.07 0.592000 0.8415030
136 12876969 Not In Discovery HOOK2 -0.07 0.592000 0.8415030
134 12876993 Not In Discovery HOOK2 -0.07 0.595000 0.8415030
144 12876911 Not In Discovery HOOK2 -0.07 0.596000 0.8415030
186 33048433 Not In Discovery HLA-DPB1 -0.07 0.596000 0.8415030
174 1178182 Not In Discovery FAM132A -0.07 0.597000 0.8415030
185 33048423 Not In Discovery HLA-DPB1 -0.07 0.597000 0.8415030
137 12876948 Not In Discovery HOOK2 -0.07 0.603000 0.8415030
139 12876944 Not In Discovery HOOK2 -0.07 0.604000 0.8415030
141 12876937 Not In Discovery HOOK2 -0.07 0.604000 0.8415030
24 67361896 Not In Discovery SMAD3 0.07 0.605000 0.8415030
140 12876942 Not In Discovery HOOK2 -0.07 0.606000 0.8415030
132 12877001 cg11738485 HOOK2 -0.07 0.607000 0.8415030
142 12876926 Not In Discovery HOOK2 -0.06 0.608000 0.8415030
138 12876946 Not In Discovery HOOK2 -0.06 0.610000 0.8415030
201 33048581 Not In Discovery HLA-DPB1 -0.07 0.611000 0.8415030
80 30039476 cg10930308 RNF39 -0.06 0.612000 0.8415030
183 92418017 Not In Discovery BRDT -0.06 0.612000 0.8415030
143 12876918 Not In Discovery HOOK2 -0.06 0.615000 0.8415030
89 12877188 cg23899408 HOOK2 -0.06 0.619000 0.8415030
76 30039432 cg13401893 RNF39 -0.06 0.622000 0.8415030
90 12877201 Not In Discovery HOOK2 -0.06 0.625000 0.8415030
92 12877235 Not In Discovery HOOK2 -0.06 0.625000 0.8415030
196 33048549 Not In Discovery HLA-DPB1 -0.06 0.632000 0.8415030
91 12877215 Not In Discovery HOOK2 -0.06 0.642000 0.8415030
184 33048417 Not In Discovery HLA-DPB1 -0.06 0.642000 0.8415030
2 42798698 Not In Discovery MX1 -0.06 0.643000 0.8415030
62 30039307 Not In Discovery RNF39 -0.06 0.650000 0.8415030
129 38805732 cg02016764 TLR1 0.06 0.654000 0.8415030
87 12877107 Not In Discovery HOOK2 -0.06 0.655000 0.8415030
94 92414650 Not In Discovery BRDT -0.06 0.660000 0.8415030
75 30039418 Not In Discovery RNF39 -0.06 0.661000 0.8415030
99 92414751 Not In Discovery BRDT -0.05 0.668000 0.8415030
192 33048529 cg06437840 HLA-DPB1 -0.05 0.669000 0.8415030
38 30039151 cg18930910 RNF39 0.05 0.673000 0.8415030
93 12877276 Not In Discovery HOOK2 -0.05 0.674000 0.8415030
86 12877099 Not In Discovery HOOK2 -0.05 0.678000 0.8415176
88 12877138 Not In Discovery HOOK2 -0.05 0.687000 0.8477018
37 30039142 cg00947782 RNF39 0.05 0.696000 0.8488786
73 30039411 Not In Discovery RNF39 0.05 0.696000 0.8488786
61 30039303 Not In Discovery RNF39 -0.05 0.704000 0.8537011
193 33048540 cg14870156 HLA-DPB1 -0.05 0.720000 0.8681143
4 42798733 Not In Discovery MX1 -0.04 0.729000 0.8739716
178 1178136 Not In Discovery FAM132A -0.04 0.734000 0.8749944
191 33048502 cg26645432 HLA-DPB1 -0.04 0.747000 0.8803011
195 33048544 Not In Discovery HLA-DPB1 -0.04 0.756000 0.8803011
54 76145628 Not In Discovery UPK3B -0.04 0.759000 0.8803011
209 79085765 cg00855901 IFI44L -0.04 0.759000 0.8803011
69 30039376 cg15877520 RNF39 -0.04 0.771000 0.8803011
60 30039278 Not In Discovery RNF39 -0.04 0.774000 0.8803011
70 30039380 cg13918754 RNF39 -0.04 0.775000 0.8803011
65 30039349 Not In Discovery RNF39 -0.04 0.776000 0.8803011
79 30039466 cg16078649 RNF39 -0.04 0.776000 0.8803011
55 76145620 Not In Discovery UPK3B -0.03 0.787000 0.8880053
118 37383713 Not In Discovery EIF2AK2 -0.03 0.806000 0.8995263
176 1178162 Not In Discovery FAM132A 0.03 0.806000 0.8995263
197 33048555 cg19990651 HLA-DPB1 -0.03 0.810000 0.8995263
189 33048483 cg03229061 HLA-DPB1 0.03 0.815000 0.9003403
188 33048469 cg10850215 HLA-DPB1 -0.03 0.827000 0.9021327
95 92414661 Not In Discovery BRDT -0.03 0.833000 0.9021327
36 30039132 Not In Discovery RNF39 0.03 0.835000 0.9021327
64 30039323 Not In Discovery RNF39 -0.03 0.838000 0.9021327
200 33048575 Not In Discovery HLA-DPB1 -0.03 0.838000 0.9021327
177 1178150 Not In Discovery FAM132A 0.02 0.848000 0.9068737
74 30039415 Not In Discovery RNF39 -0.02 0.851000 0.9068737
59 30039274 Not In Discovery RNF39 -0.02 0.857000 0.9086784
179 1178118 Not In Discovery FAM132A 0.02 0.866000 0.9136300
49 76145702 Not In Discovery UPK3B 0.02 0.876000 0.9167586
78 30039442 cg10568066 RNF39 -0.02 0.879000 0.9167586
66 30039354 Not In Discovery RNF39 -0.02 0.882000 0.9167586
63 30039313 Not In Discovery RNF39 -0.02 0.901000 0.9319167
190 33048485 cg17588455 HLA-DPB1 -0.01 0.910000 0.9366341
98 92414737 cg13299824 BRDT -0.01 0.918000 0.9402816
71 30039403 cg09279736 RNF39 -0.01 0.949000 0.9673382
77 30039435 cg12633154 RNF39 -0.01 0.957000 0.9708029
97 92414722 cg14732540 BRDT 0.00 0.972000 0.9813014
96 92414719 Not In Discovery BRDT 0.00 0.984000 0.9870000
116 37383623 Not In Discovery EIF2AK2 0.00 0.987000 0.9870000

5.7.4 Figure32:Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells

5.8 Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells

5.8.1 Table 33:Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells

CpGs CpGnames Gene Corr.alpha P.value FDR
108 122281939 cg08122652 PARP9 -0.38 0.00257 0.4272750
77 21572657 cg18719665 TTC39C 0.35 0.00405 0.4272750
109 122281975 cg00959259 PARP9 -0.34 0.00766 0.5387533
78 21572635 cg05401069 TTC39C 0.32 0.01040 0.5486000
79 21572623 cg12639429 TTC39C 0.29 0.01790 0.5886900
173 1178150 Not In Discovery FAM132A -0.30 0.01840 0.5886900
103 62199034 cg17593958 HELZ2 0.31 0.02080 0.5886900
194 33048558 cg01132696 HLA-DPB1 -0.30 0.02410 0.5886900
119 37383568 cg17326313 EIF2AK2 -0.28 0.02690 0.5886900
6 42798749 Not In Discovery MX1 -0.27 0.02790 0.5886900
196 33048575 Not In Discovery HLA-DPB1 -0.27 0.03990 0.7284524
16 42798863 Not In Discovery MX1 -0.25 0.04670 0.7284524
198 33048592 Not In Discovery HLA-DPB1 -0.25 0.05460 0.7284524
192 33048549 Not In Discovery HLA-DPB1 -0.24 0.06520 0.7284524
211 67361896 Not In Discovery SMAD3 0.24 0.06920 0.7284524
191 33048544 Not In Discovery HLA-DPB1 -0.24 0.07420 0.7284524
13 42798837 Not In Discovery MX1 -0.22 0.07640 0.7284524
169 1178192 Not In Discovery FAM132A -0.22 0.07950 0.7284524
100 92414770 Not In Discovery BRDT -0.22 0.08620 0.7284524
81 313408 Not In Discovery IFITM1 -0.22 0.08640 0.7284524
197 33048581 Not In Discovery HLA-DPB1 -0.23 0.08870 0.7284524
15 42798857 Not In Discovery MX1 -0.21 0.08920 0.7284524
102 92414793 Not In Discovery BRDT -0.21 0.09260 0.7284524
183 33048444 Not In Discovery HLA-DPB1 -0.22 0.09630 0.7284524
187 33048502 cg26645432 HLA-DPB1 -0.22 0.09770 0.7284524
99 92414751 Not In Discovery BRDT -0.21 0.09860 0.7284524
8 42798781 Not In Discovery MX1 -0.21 0.10100 0.7284524
101 92414782 cg02935097 BRDT -0.20 0.10900 0.7284524
47 76145689 Not In Discovery UPK3B 0.20 0.11200 0.7284524
4 42798733 Not In Discovery MX1 -0.20 0.11300 0.7284524
80 313354 cg11694510 IFITM1 -0.20 0.12100 0.7284524
195 33048571 Not In Discovery HLA-DPB1 -0.20 0.12300 0.7284524
189 33048540 cg14870156 HLA-DPB1 -0.20 0.12500 0.7284524
46 76145693 Not In Discovery UPK3B 0.19 0.12600 0.7284524
193 33048555 cg19990651 HLA-DPB1 -0.20 0.13000 0.7284524
98 92414737 cg13299824 BRDT -0.19 0.13500 0.7284524
12 42798829 Not In Discovery MX1 -0.19 0.13700 0.7284524
48 76145673 cg05372444 UPK3B 0.19 0.14000 0.7284524
170 1178182 Not In Discovery FAM132A -0.19 0.14000 0.7284524
180 33048417 Not In Discovery HLA-DPB1 -0.19 0.14300 0.7284524
95 92414661 Not In Discovery BRDT -0.19 0.14400 0.7284524
14 42798847 Not In Discovery MX1 -0.18 0.14500 0.7284524
106 62199181 cg06064964 HELZ2 0.19 0.15200 0.7289091
171 1178172 Not In Discovery FAM132A -0.18 0.15200 0.7289091
188 33048529 cg06437840 HLA-DPB1 -0.18 0.16800 0.7843696
168 1178202 Not In Discovery FAM132A -0.17 0.17100 0.7843696
10 42798816 Not In Discovery MX1 -0.17 0.18400 0.8132292
9 42798813 Not In Discovery MX1 -0.17 0.18500 0.8132292
20 30039132 Not In Discovery RNF39 0.17 0.19600 0.8382973
19 30039130 Not In Discovery RNF39 0.16 0.20500 0.8382973
182 33048433 Not In Discovery HLA-DPB1 -0.17 0.21100 0.8382973
52 76145606 Not In Discovery UPK3B 0.15 0.22600 0.8382973
94 92414650 Not In Discovery BRDT -0.15 0.22700 0.8382973
97 92414722 cg14732540 BRDT -0.15 0.23000 0.8382973
11 42798818 Not In Discovery MX1 -0.15 0.23800 0.8382973
3 42798723 Not In Discovery MX1 -0.15 0.23900 0.8382973
199 33048602 Not In Discovery HLA-DPB1 -0.16 0.24000 0.8382973
96 92414719 Not In Discovery BRDT -0.15 0.24500 0.8382973
124 37383730 Not In Discovery EIF2AK2 -0.14 0.27800 0.8382973
5 42798747 cg08924203 MX1 -0.14 0.28000 0.8382973
32 33048286 cg09234582 HLA-DPB1 -0.14 0.28300 0.8382973
181 33048423 Not In Discovery HLA-DPB1 -0.14 0.29000 0.8382973
107 62199190 cg09844573 HELZ2 0.14 0.29100 0.8382973
202 79085713 cg17980508 IFI44L -0.14 0.29600 0.8382973
25 30039186 Not In Discovery RNF39 0.13 0.29700 0.8382973
22 30039151 cg18930910 RNF39 0.13 0.30300 0.8382973
71 30039418 Not In Discovery RNF39 -0.12 0.33100 0.8382973
203 79085765 cg00855901 IFI44L -0.13 0.33500 0.8382973
18 30039127 Not In Discovery RNF39 0.12 0.33900 0.8382973
33 33048291 cg25045942 HLA-DPB1 -0.12 0.34000 0.8382973
89 12877276 Not In Discovery HOOK2 -0.12 0.34300 0.8382973
24 30039175 cg03343571 RNF39 0.12 0.34600 0.8382973
184 33048469 cg10850215 HLA-DPB1 -0.12 0.35200 0.8382973
34 33048310 cg13349035 HLA-DPB1 -0.12 0.36200 0.8382973
179 92418017 Not In Discovery BRDT -0.11 0.37000 0.8382973
104 62199061 Not In Discovery HELZ2 0.12 0.38000 0.8382973
40 75953935 cg19367436 COX7A2 0.11 0.38800 0.8382973
200 79085586 cg03607951 IFI44L -0.11 0.38900 0.8382973
51 76145620 Not In Discovery UPK3B 0.11 0.39700 0.8382973
76 30039476 cg10930308 RNF39 -0.11 0.40500 0.8382973
83 12877107 Not In Discovery HOOK2 -0.10 0.41400 0.8382973
21 30039142 cg00947782 RNF39 0.10 0.41700 0.8382973
82 12877099 Not In Discovery HOOK2 -0.10 0.42000 0.8382973
140 12876911 Not In Discovery HOOK2 -0.10 0.42800 0.8382973
139 12876918 Not In Discovery HOOK2 -0.10 0.43000 0.8382973
53 76145589 Not In Discovery UPK3B -0.10 0.43300 0.8382973
121 37383623 Not In Discovery EIF2AK2 -0.10 0.43400 0.8382973
136 12876942 Not In Discovery HOOK2 -0.10 0.43800 0.8382973
23 30039158 Not In Discovery RNF39 0.10 0.43900 0.8382973
135 12876944 Not In Discovery HOOK2 -0.10 0.44100 0.8382973
154 179740906 Not In Discovery GFPT2 0.10 0.44100 0.8382973
17 30039123 Not In Discovery RNF39 0.10 0.44200 0.8382973
208 67361773 cg24961286 SMAD3 0.10 0.44300 0.8382973
36 75953821 Not In Discovery COX7A2 0.10 0.44900 0.8382973
132 12876969 Not In Discovery HOOK2 -0.10 0.44900 0.8382973
138 12876926 Not In Discovery HOOK2 -0.10 0.44900 0.8382973
151 179740920 Not In Discovery GFPT2 0.10 0.44900 0.8382973
134 12876946 Not In Discovery HOOK2 -0.10 0.45100 0.8382973
131 12876987 Not In Discovery HOOK2 -0.09 0.45500 0.8382973
84 12877138 Not In Discovery HOOK2 -0.09 0.45700 0.8382973
128 12877001 cg11738485 HOOK2 -0.09 0.45900 0.8382973
133 12876948 Not In Discovery HOOK2 -0.09 0.46300 0.8382973
137 12876937 Not In Discovery HOOK2 -0.09 0.46300 0.8382973
87 12877215 Not In Discovery HOOK2 -0.09 0.46600 0.8382973
88 12877235 Not In Discovery HOOK2 -0.09 0.46600 0.8382973
29 30039232 Not In Discovery RNF39 0.09 0.47000 0.8382973
129 12876997 Not In Discovery HOOK2 -0.09 0.47200 0.8382973
130 12876993 Not In Discovery HOOK2 -0.09 0.47500 0.8382973
156 179740888 Not In Discovery GFPT2 0.09 0.47600 0.8382973
55 30039274 Not In Discovery RNF39 -0.09 0.47800 0.8382973
30 30039235 Not In Discovery RNF39 0.09 0.48100 0.8382973
146 179740963 Not In Discovery GFPT2 0.09 0.48400 0.8382973
209 67361798 Not In Discovery SMAD3 0.09 0.48800 0.8382973
112 179741101 Not In Discovery GFPT2 0.09 0.49000 0.8382973
147 179740957 Not In Discovery GFPT2 0.09 0.49000 0.8382973
145 179740970 Not In Discovery GFPT2 0.09 0.49400 0.8382973
127 12877020 Not In Discovery HOOK2 -0.09 0.49900 0.8382973
148 179740955 Not In Discovery GFPT2 0.09 0.50400 0.8382973
31 30039239 Not In Discovery RNF39 0.09 0.50500 0.8382973
142 179740999 Not In Discovery GFPT2 0.08 0.50900 0.8382973
167 1178207 Not In Discovery FAM132A -0.08 0.51000 0.8382973
141 179741008 Not In Discovery GFPT2 0.08 0.52200 0.8382973
155 179740900 Not In Discovery GFPT2 0.08 0.52300 0.8382973
67 30039403 cg09279736 RNF39 -0.08 0.52600 0.8382973
152 179740918 Not In Discovery GFPT2 0.08 0.52600 0.8382973
143 179740994 Not In Discovery GFPT2 0.08 0.52900 0.8382973
57 30039303 Not In Discovery RNF39 -0.08 0.53500 0.8382973
153 179740915 cg13944838 GFPT2 0.08 0.53700 0.8382973
105 62199156 cg11779113 HELZ2 0.08 0.54700 0.8382973
150 179740935 Not In Discovery GFPT2 0.08 0.55200 0.8382973
149 179740940 Not In Discovery GFPT2 0.08 0.55400 0.8382973
114 179741067 Not In Discovery GFPT2 0.08 0.55500 0.8382973
120 37383588 Not In Discovery EIF2AK2 -0.08 0.55500 0.8382973
144 179740992 Not In Discovery GFPT2 0.07 0.55600 0.8382973
162 179740840 Not In Discovery GFPT2 0.07 0.55800 0.8382973
86 12877201 Not In Discovery HOOK2 -0.07 0.55900 0.8382973
26 30039202 Not In Discovery RNF39 0.07 0.56000 0.8382973
1 42798695 Not In Discovery MX1 -0.07 0.56800 0.8382973
85 12877188 cg23899408 HOOK2 -0.07 0.56800 0.8382973
66 30039380 cg13918754 RNF39 -0.07 0.56900 0.8382973
158 179740867 Not In Discovery GFPT2 0.07 0.57000 0.8382973
49 76145633 cg16453056 UPK3B 0.07 0.57300 0.8382973
157 179740869 Not In Discovery GFPT2 0.07 0.57300 0.8382973
186 33048485 cg17588455 HLA-DPB1 -0.07 0.58000 0.8382973
110 179741121 cg02891314 GFPT2 0.07 0.58200 0.8382973
161 179740852 Not In Discovery GFPT2 0.07 0.58200 0.8382973
64 30039374 cg20249327 RNF39 -0.07 0.58700 0.8382973
41 75953937 Not In Discovery COX7A2 0.07 0.58800 0.8382973
65 30039376 cg15877520 RNF39 -0.07 0.59700 0.8403198
117 179741042 Not In Discovery GFPT2 0.07 0.59900 0.8403198
2 42798698 Not In Discovery MX1 -0.07 0.60200 0.8403198
116 179741060 Not In Discovery GFPT2 0.07 0.61000 0.8403198
115 179741063 Not In Discovery GFPT2 0.06 0.61600 0.8403198
126 38805839 Not In Discovery TLR1 -0.10 0.61700 0.8403198
185 33048483 cg03229061 HLA-DPB1 -0.07 0.61800 0.8403198
7 42798765 Not In Discovery MX1 -0.06 0.62600 0.8403198
113 179741081 Not In Discovery GFPT2 0.06 0.62600 0.8403198
164 179740825 Not In Discovery GFPT2 0.06 0.63600 0.8403198
172 1178162 Not In Discovery FAM132A -0.06 0.63600 0.8403198
69 30039411 Not In Discovery RNF39 -0.06 0.63900 0.8403198
28 30039208 Not In Discovery RNF39 0.06 0.64700 0.8403198
37 75953829 Not In Discovery COX7A2 0.06 0.65200 0.8403198
165 179740822 Not In Discovery GFPT2 0.06 0.65800 0.8403198
111 179741105 cg23248424 GFPT2 0.06 0.66400 0.8403198
50 76145628 Not In Discovery UPK3B 0.05 0.66900 0.8403198
159 179740861 Not In Discovery GFPT2 0.05 0.67000 0.8403198
163 179740832 Not In Discovery GFPT2 0.05 0.67300 0.8403198
123 37383713 Not In Discovery EIF2AK2 0.05 0.67600 0.8403198
204 312419 Not In Discovery IFITM1 -0.06 0.67700 0.8403198
91 75954053 cg25716013 COX7A2 -0.05 0.68100 0.8403198
206 312463 Not In Discovery IFITM1 -0.06 0.68400 0.8403198
38 75953853 cg06809298 COX7A2 0.05 0.68500 0.8403198
58 30039307 Not In Discovery RNF39 -0.05 0.69000 0.8403829
160 179740855 Not In Discovery GFPT2 0.05 0.69600 0.8403829
178 92417998 cg01081438 BRDT 0.05 0.69700 0.8403829
118 179741039 Not In Discovery GFPT2 0.05 0.70300 0.8404438
210 67361821 Not In Discovery SMAD3 0.05 0.70600 0.8404438
45 76145702 Not In Discovery UPK3B -0.05 0.70900 0.8404438
59 30039313 Not In Discovery RNF39 -0.05 0.71500 0.8428212
56 30039278 Not In Discovery RNF39 -0.05 0.72400 0.8486889
54 30039271 Not In Discovery RNF39 -0.04 0.73200 0.8509180
73 30039435 cg12633154 RNF39 -0.04 0.73500 0.8509180
68 30039408 cg07382347 RNF39 -0.04 0.73800 0.8509180
176 1178105 Not In Discovery FAM132A -0.04 0.75500 0.8657880
207 312518 cg05432003 IFITM1 0.06 0.76600 0.8736541
62 30039354 Not In Discovery RNF39 -0.04 0.78500 0.8855266
42 75953960 Not In Discovery COX7A2 0.04 0.78700 0.8855266
174 1178136 Not In Discovery FAM132A 0.03 0.78900 0.8855266
35 33048370 Not In Discovery HLA-DPB1 -0.03 0.80200 0.8953545
27 30039206 Not In Discovery RNF39 0.03 0.82000 0.9069686
60 30039323 Not In Discovery RNF39 -0.03 0.82100 0.9069686
90 75954022 Not In Discovery COX7A2 -0.03 0.82800 0.9099375
39 75953883 Not In Discovery COX7A2 0.03 0.83500 0.9128756
93 75954122 Not In Discovery COX7A2 -0.02 0.84700 0.9212216
72 30039432 cg13401893 RNF39 -0.02 0.85500 0.9251538
74 30039442 cg10568066 RNF39 -0.02 0.87000 0.9313838
63 30039364 Not In Discovery RNF39 0.02 0.87200 0.9313838
177 1178086 Not In Discovery FAM132A -0.02 0.87400 0.9313838
61 30039349 Not In Discovery RNF39 -0.02 0.88600 0.9394271
190 33048542 Not In Discovery HLA-DPB1 -0.02 0.89700 0.9406650
205 312434 Not In Discovery IFITM1 -0.02 0.89900 0.9406650
44 76145717 Not In Discovery UPK3B 0.02 0.90500 0.9406650
175 1178118 Not In Discovery FAM132A -0.02 0.90500 0.9406650
125 38805732 cg02016764 TLR1 0.02 0.91200 0.9428098
92 75954118 Not In Discovery COX7A2 -0.01 0.91600 0.9428098
201 79085647 Not In Discovery IFI44L -0.01 0.94200 0.9648641
43 75953974 Not In Discovery COX7A2 0.01 0.95700 0.9754928
166 1178246 cg24345856 FAM132A 0.00 0.96900 0.9829760
70 30039415 Not In Discovery RNF39 0.00 0.98000 0.9893780
75 30039466 cg16078649 RNF39 0.00 0.99400 0.9960000
122 37383679 Not In Discovery EIF2AK2 0.00 0.99600 0.9960000

5.8.2 Figure33:Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells

5.9 Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells

5.9.1 Table 34:Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells

CpGs CpGnames Gene Corr.beta P.value FDR
108 122281939 cg08122652 PARP9 -0.46 0.000181 0.0381910
109 122281975 cg00959259 PARP9 -0.44 0.000420 0.0443100
96 92414719 Not In Discovery BRDT -0.40 0.001040 0.0731467
119 37383568 cg17326313 EIF2AK2 -0.39 0.001700 0.0773667
77 21572657 cg18719665 TTC39C 0.38 0.001960 0.0773667
98 92414737 cg13299824 BRDT -0.38 0.002200 0.0773667
97 92414722 cg14732540 BRDT -0.36 0.003710 0.1095693
78 21572635 cg05401069 TTC39C 0.35 0.004630 0.1095693
94 92414650 Not In Discovery BRDT -0.34 0.006390 0.1095693
79 21572623 cg12639429 TTC39C 0.33 0.006400 0.1095693
99 92414751 Not In Discovery BRDT -0.34 0.006790 0.1095693
100 92414770 Not In Discovery BRDT -0.34 0.007060 0.1095693
101 92414782 cg02935097 BRDT -0.34 0.007130 0.1095693
95 92414661 Not In Discovery BRDT -0.34 0.007270 0.1095693
102 92414793 Not In Discovery BRDT -0.33 0.008290 0.1166127
49 76145633 cg16453056 UPK3B 0.31 0.012600 0.1661625
103 62199034 cg17593958 HELZ2 0.33 0.013900 0.1725235
170 1178182 Not In Discovery FAM132A -0.27 0.033200 0.3891778
31 30039239 Not In Discovery RNF39 0.26 0.037200 0.4131158
22 30039151 cg18930910 RNF39 0.24 0.056600 0.5266208
24 30039175 cg03343571 RNF39 0.24 0.057500 0.5266208
30 30039235 Not In Discovery RNF39 0.24 0.058100 0.5266208
120 37383588 Not In Discovery EIF2AK2 -0.24 0.059700 0.5266208
171 1178172 Not In Discovery FAM132A -0.24 0.059900 0.5266208
63 30039364 Not In Discovery RNF39 0.22 0.089200 0.7493458
173 1178150 Not In Discovery FAM132A -0.21 0.092900 0.7493458
29 30039232 Not In Discovery RNF39 0.21 0.103000 0.7493458
39 75953883 Not In Discovery COX7A2 -0.21 0.104000 0.7493458
81 313408 Not In Discovery IFITM1 -0.20 0.108000 0.7493458
51 76145620 Not In Discovery UPK3B 0.20 0.116000 0.7493458
15 42798857 Not In Discovery MX1 -0.20 0.120000 0.7493458
47 76145689 Not In Discovery UPK3B 0.19 0.127000 0.7493458
178 92417998 cg01081438 BRDT 0.19 0.128000 0.7493458
168 1178202 Not In Discovery FAM132A -0.19 0.130000 0.7493458
26 30039202 Not In Discovery RNF39 0.19 0.133000 0.7493458
27 30039206 Not In Discovery RNF39 0.19 0.136000 0.7493458
16 42798863 Not In Discovery MX1 -0.19 0.139000 0.7493458
204 312419 Not In Discovery IFITM1 -0.23 0.142000 0.7493458
106 62199181 cg06064964 HELZ2 0.20 0.148000 0.7493458
23 30039158 Not In Discovery RNF39 0.18 0.151000 0.7493458
209 67361798 Not In Discovery SMAD3 0.19 0.160000 0.7493458
25 30039186 Not In Discovery RNF39 0.18 0.162000 0.7493458
38 75953853 cg06809298 COX7A2 -0.18 0.166000 0.7493458
13 42798837 Not In Discovery MX1 -0.17 0.169000 0.7493458
12 42798829 Not In Discovery MX1 -0.17 0.171000 0.7493458
48 76145673 cg05372444 UPK3B 0.17 0.174000 0.7493458
80 313354 cg11694510 IFITM1 -0.17 0.174000 0.7493458
113 179741081 Not In Discovery GFPT2 -0.17 0.193000 0.7493458
202 79085713 cg17980508 IFI44L -0.17 0.205000 0.7493458
90 75954022 Not In Discovery COX7A2 -0.16 0.210000 0.7493458
111 179741105 cg23248424 GFPT2 -0.16 0.217000 0.7493458
152 179740918 Not In Discovery GFPT2 -0.15 0.225000 0.7493458
21 30039142 cg00947782 RNF39 0.15 0.229000 0.7493458
34 33048310 cg13349035 HLA-DPB1 -0.15 0.229000 0.7493458
116 179741060 Not In Discovery GFPT2 -0.15 0.235000 0.7493458
5 42798747 cg08924203 MX1 -0.15 0.239000 0.7493458
43 75953974 Not In Discovery COX7A2 -0.15 0.240000 0.7493458
110 179741121 cg02891314 GFPT2 -0.15 0.246000 0.7493458
166 1178246 cg24345856 FAM132A 0.15 0.249000 0.7493458
37 75953829 Not In Discovery COX7A2 -0.15 0.251000 0.7493458
117 179741042 Not In Discovery GFPT2 -0.15 0.252000 0.7493458
114 179741067 Not In Discovery GFPT2 -0.15 0.256000 0.7493458
124 37383730 Not In Discovery EIF2AK2 -0.15 0.264000 0.7493458
118 179741039 Not In Discovery GFPT2 -0.14 0.270000 0.7493458
141 179741008 Not In Discovery GFPT2 -0.14 0.274000 0.7493458
112 179741101 Not In Discovery GFPT2 -0.14 0.275000 0.7493458
104 62199061 Not In Discovery HELZ2 0.15 0.276000 0.7493458
149 179740940 Not In Discovery GFPT2 -0.14 0.276000 0.7493458
18 30039127 Not In Discovery RNF39 0.14 0.282000 0.7493458
44 76145717 Not In Discovery UPK3B 0.14 0.290000 0.7493458
165 179740822 Not In Discovery GFPT2 -0.13 0.292000 0.7493458
7 42798765 Not In Discovery MX1 -0.13 0.293000 0.7493458
121 37383623 Not In Discovery EIF2AK2 -0.14 0.293000 0.7493458
145 179740970 Not In Discovery GFPT2 -0.13 0.293000 0.7493458
151 179740920 Not In Discovery GFPT2 -0.13 0.299000 0.7493458
153 179740915 cg13944838 GFPT2 -0.13 0.299000 0.7493458
196 33048575 Not In Discovery HLA-DPB1 -0.14 0.303000 0.7493458
91 75954053 cg25716013 COX7A2 -0.13 0.304000 0.7493458
172 1178162 Not In Discovery FAM132A -0.13 0.304000 0.7493458
155 179740900 Not In Discovery GFPT2 -0.13 0.305000 0.7493458
146 179740963 Not In Discovery GFPT2 -0.13 0.312000 0.7493458
14 42798847 Not In Discovery MX1 -0.13 0.315000 0.7493458
8 42798781 Not In Discovery MX1 -0.13 0.318000 0.7493458
148 179740955 Not In Discovery GFPT2 -0.13 0.321000 0.7493458
35 33048370 Not In Discovery HLA-DPB1 -0.13 0.325000 0.7493458
115 179741063 Not In Discovery GFPT2 -0.13 0.325000 0.7493458
199 33048602 Not In Discovery HLA-DPB1 -0.13 0.329000 0.7493458
150 179740935 Not In Discovery GFPT2 -0.12 0.332000 0.7493458
105 62199156 cg11779113 HELZ2 0.13 0.333000 0.7493458
156 179740888 Not In Discovery GFPT2 -0.12 0.333000 0.7493458
3 42798723 Not In Discovery MX1 -0.12 0.336000 0.7493458
143 179740994 Not In Discovery GFPT2 -0.12 0.339000 0.7493458
144 179740992 Not In Discovery GFPT2 -0.12 0.346000 0.7493458
50 76145628 Not In Discovery UPK3B 0.12 0.348000 0.7493458
92 75954118 Not In Discovery COX7A2 -0.12 0.348000 0.7493458
122 37383679 Not In Discovery EIF2AK2 -0.12 0.349000 0.7493458
46 76145693 Not In Discovery UPK3B 0.12 0.352000 0.7493458
147 179740957 Not In Discovery GFPT2 -0.12 0.357000 0.7493458
93 75954122 Not In Discovery COX7A2 -0.12 0.361000 0.7493458
10 42798816 Not In Discovery MX1 -0.12 0.362000 0.7493458
142 179740999 Not In Discovery GFPT2 -0.12 0.365000 0.7493458
89 12877276 Not In Discovery HOOK2 -0.11 0.366000 0.7493458
28 30039208 Not In Discovery RNF39 0.12 0.367000 0.7493458
76 30039476 cg10930308 RNF39 -0.11 0.375000 0.7493458
154 179740906 Not In Discovery GFPT2 -0.11 0.378000 0.7493458
6 42798749 Not In Discovery MX1 -0.11 0.380000 0.7493458
203 79085765 cg00855901 IFI44L -0.12 0.380000 0.7493458
163 179740832 Not In Discovery GFPT2 -0.11 0.399000 0.7781835
159 179740861 Not In Discovery GFPT2 -0.11 0.402000 0.7781835
9 42798813 Not In Discovery MX1 -0.10 0.414000 0.7941273
11 42798818 Not In Discovery MX1 -0.10 0.430000 0.8029204
157 179740869 Not In Discovery GFPT2 -0.10 0.430000 0.8029204
158 179740867 Not In Discovery GFPT2 -0.10 0.430000 0.8029204
162 179740840 Not In Discovery GFPT2 -0.10 0.442000 0.8138571
189 33048540 cg14870156 HLA-DPB1 -0.10 0.447000 0.8138571
58 30039307 Not In Discovery RNF39 -0.10 0.456000 0.8138571
164 179740825 Not In Discovery GFPT2 -0.09 0.460000 0.8138571
160 179740855 Not In Discovery GFPT2 -0.09 0.491000 0.8138571
167 1178207 Not In Discovery FAM132A -0.09 0.496000 0.8138571
88 12877235 Not In Discovery HOOK2 -0.09 0.497000 0.8138571
36 75953821 Not In Discovery COX7A2 -0.09 0.498000 0.8138571
32 33048286 cg09234582 HLA-DPB1 -0.09 0.501000 0.8138571
161 179740852 Not In Discovery GFPT2 -0.09 0.501000 0.8138571
190 33048542 Not In Discovery HLA-DPB1 0.09 0.509000 0.8138571
200 79085586 cg03607951 IFI44L -0.09 0.515000 0.8138571
125 38805732 cg02016764 TLR1 0.12 0.521000 0.8138571
208 67361773 cg24961286 SMAD3 0.09 0.523000 0.8138571
54 30039271 Not In Discovery RNF39 -0.08 0.524000 0.8138571
198 33048592 Not In Discovery HLA-DPB1 -0.09 0.525000 0.8138571
52 76145606 Not In Discovery UPK3B -0.08 0.533000 0.8138571
42 75953960 Not In Discovery COX7A2 -0.08 0.538000 0.8138571
65 30039376 cg15877520 RNF39 -0.07 0.560000 0.8138571
192 33048549 Not In Discovery HLA-DPB1 -0.08 0.562000 0.8138571
210 67361821 Not In Discovery SMAD3 0.08 0.567000 0.8138571
33 33048291 cg25045942 HLA-DPB1 -0.07 0.571000 0.8138571
177 1178086 Not In Discovery FAM132A -0.07 0.579000 0.8138571
75 30039466 cg16078649 RNF39 -0.07 0.580000 0.8138571
59 30039313 Not In Discovery RNF39 -0.07 0.584000 0.8138571
62 30039354 Not In Discovery RNF39 -0.07 0.586000 0.8138571
123 37383713 Not In Discovery EIF2AK2 -0.07 0.587000 0.8138571
185 33048483 cg03229061 HLA-DPB1 -0.07 0.587000 0.8138571
136 12876942 Not In Discovery HOOK2 -0.07 0.588000 0.8138571
64 30039374 cg20249327 RNF39 -0.07 0.594000 0.8138571
181 33048423 Not In Discovery HLA-DPB1 -0.07 0.595000 0.8138571
131 12876987 Not In Discovery HOOK2 -0.07 0.597000 0.8138571
140 12876911 Not In Discovery HOOK2 -0.07 0.598000 0.8138571
129 12876997 Not In Discovery HOOK2 -0.07 0.599000 0.8138571
74 30039442 cg10568066 RNF39 0.07 0.600000 0.8138571
87 12877215 Not In Discovery HOOK2 -0.07 0.600000 0.8138571
82 12877099 Not In Discovery HOOK2 -0.07 0.601000 0.8138571
132 12876969 Not In Discovery HOOK2 -0.07 0.601000 0.8138571
138 12876926 Not In Discovery HOOK2 -0.07 0.601000 0.8138571
135 12876944 Not In Discovery HOOK2 -0.07 0.602000 0.8138571
83 12877107 Not In Discovery HOOK2 -0.07 0.603000 0.8138571
206 312463 Not In Discovery IFITM1 -0.08 0.606000 0.8138571
128 12877001 cg11738485 HOOK2 -0.06 0.610000 0.8138571
134 12876946 Not In Discovery HOOK2 -0.06 0.612000 0.8138571
130 12876993 Not In Discovery HOOK2 -0.06 0.614000 0.8138571
137 12876937 Not In Discovery HOOK2 -0.06 0.614000 0.8138571
133 12876948 Not In Discovery HOOK2 -0.06 0.618000 0.8138571
139 12876918 Not In Discovery HOOK2 -0.06 0.621000 0.8138571
19 30039130 Not In Discovery RNF39 0.06 0.626000 0.8153457
127 12877020 Not In Discovery HOOK2 -0.06 0.631000 0.8160361
40 75953935 cg19367436 COX7A2 -0.06 0.639000 0.8160361
66 30039380 cg13918754 RNF39 -0.06 0.641000 0.8160361
86 12877201 Not In Discovery HOOK2 -0.06 0.642000 0.8160361
53 76145589 Not In Discovery UPK3B 0.06 0.648000 0.8176250
4 42798733 Not In Discovery MX1 -0.06 0.651000 0.8176250
20 30039132 Not In Discovery RNF39 0.06 0.660000 0.8183873
84 12877138 Not In Discovery HOOK2 -0.06 0.663000 0.8183873
17 30039123 Not In Discovery RNF39 0.06 0.667000 0.8183873
175 1178118 Not In Discovery FAM132A 0.05 0.669000 0.8183873
1 42798695 Not In Discovery MX1 0.05 0.671000 0.8183873
183 33048444 Not In Discovery HLA-DPB1 -0.05 0.686000 0.8318736
194 33048558 cg01132696 HLA-DPB1 -0.05 0.695000 0.8368068
207 312518 cg05432003 IFITM1 0.08 0.698000 0.8368068
41 75953937 Not In Discovery COX7A2 -0.05 0.709000 0.8451921
193 33048555 cg19990651 HLA-DPB1 -0.05 0.718000 0.8511124
57 30039303 Not In Discovery RNF39 -0.05 0.726000 0.8522056
70 30039415 Not In Discovery RNF39 -0.04 0.727000 0.8522056
107 62199190 cg09844573 HELZ2 0.04 0.745000 0.8654385
182 33048433 Not In Discovery HLA-DPB1 -0.04 0.753000 0.8654385
60 30039323 Not In Discovery RNF39 -0.04 0.754000 0.8654385
174 1178136 Not In Discovery FAM132A -0.04 0.764000 0.8654385
211 67361896 Not In Discovery SMAD3 0.04 0.765000 0.8654385
71 30039418 Not In Discovery RNF39 -0.04 0.766000 0.8654385
85 12877188 cg23899408 HOOK2 -0.04 0.767000 0.8654385
72 30039432 cg13401893 RNF39 0.04 0.774000 0.8686915
69 30039411 Not In Discovery RNF39 -0.03 0.803000 0.8964709
126 38805839 Not In Discovery TLR1 0.04 0.822000 0.9067590
56 30039278 Not In Discovery RNF39 -0.03 0.832000 0.9067590
55 30039274 Not In Discovery RNF39 -0.03 0.833000 0.9067590
186 33048485 cg17588455 HLA-DPB1 -0.03 0.836000 0.9067590
188 33048529 cg06437840 HLA-DPB1 -0.03 0.838000 0.9067590
197 33048581 Not In Discovery HLA-DPB1 -0.03 0.838000 0.9067590
180 33048417 Not In Discovery HLA-DPB1 0.02 0.853000 0.9136193
205 312434 Not In Discovery IFITM1 0.03 0.853000 0.9136193
176 1178105 Not In Discovery FAM132A -0.02 0.860000 0.9150402
195 33048571 Not In Discovery HLA-DPB1 -0.02 0.863000 0.9150402
2 42798698 Not In Discovery MX1 -0.02 0.876000 0.9202525
179 92418017 Not In Discovery BRDT -0.02 0.878000 0.9202525
184 33048469 cg10850215 HLA-DPB1 0.02 0.881000 0.9202525
73 30039435 cg12633154 RNF39 -0.02 0.902000 0.9375468
68 30039408 cg07382347 RNF39 -0.01 0.909000 0.9401912
187 33048502 cg26645432 HLA-DPB1 -0.01 0.918000 0.9448683
169 1178192 Not In Discovery FAM132A -0.01 0.926000 0.9484757
45 76145702 Not In Discovery UPK3B -0.01 0.939000 0.9571449
201 79085647 Not In Discovery IFI44L -0.01 0.950000 0.9611100
67 30039403 cg09279736 RNF39 -0.01 0.952000 0.9611100
61 30039349 Not In Discovery RNF39 -0.01 0.968000 0.9726095
191 33048544 Not In Discovery HLA-DPB1 0.00 0.973000 0.9730000

5.9.2 Figure34:Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells

5.10 PartIV Summary:

In this part, we explored the differential serum content of type I IFN alpha and IFN beta between SSc patients and Controls. According to our dataset, we found significantly higher serum type I IFN alpha as well as beta levels in SSc patients, indicating its abnormalty in SSc pathogenesis, and it was concordant with previous datasets as well as the datasets in SLE patients. In addition to the differential content of serum type I IFN, we also explored its correlation with gene expression and methylation. In general, we found that, the IFN related genes showed increased gene expression as the increase of type I IFN alpha/beta, and showed decreased gene methylation as the increase of type I IFN alpha/beta. This results was concordant with the previous Part III result that suggested the negative correlation between gene expression and methylation in IFN related genes.

6 Part V: INF treating for Cell Line

6.1 The Jurket Cell Analysis

Gene POS Avg.Base Normal IFN.a.6 IFN.b.6 IFN.ab.6 IFN.a.12 IFN.b.12 IFN.ab.12 Min.Fold Max.Fold
239 IFITM1_ 312518 49.56863 0.1808279 0.2186960 0.1362536 0.1658155 0.1542028 0.1497752 0.1617978 0.7534987 1.2094153
226 HLA-DPB1_ 33048542 6509.50943 0.0036763 0.0037293 0.0032093 0.0028211 0.0039949 0.0043449 0.0039498 0.7673814 1.1818781
151 EIF2AK2_ 37383730 8206.24528 0.0171492 0.0163116 0.0152293 0.0133239 0.0168189 0.0140194 0.0162482 0.7769373 0.9807383
149 EIF2AK2_ 37383679 8206.28302 0.0185175 0.0173858 0.0161690 0.0171169 0.0149471 0.0165643 0.0169265 0.8071895 0.9388868
148 EIF2AK2_ 37383623 8218.43396 0.0144687 0.0136239 0.0132008 0.0120720 0.0116902 0.0141835 0.0151972 0.8079680 1.0503529
241 IFI44L_ 79085647 27.94340 0.2645299 0.3018890 0.4836957 0.2175325 0.3421325 0.3544292 0.3333333 0.8223360 1.8285102
214 BRDT_2 92417998 2442.32075 0.0385421 0.0394334 0.0433417 0.0633226 0.0330661 0.0361959 0.0358999 0.8579229 1.6429488
202 FAM132A_ 1178246 2862.20755 0.0735571 0.0638543 0.0727095 0.0688066 0.0721988 0.0841401 0.0785009 0.8680915 1.1438747
132 HELZ2_ 62199190 2844.45283 0.0110791 0.0104221 0.0097193 0.0096732 0.0128305 0.0127949 0.0139698 0.8731008 1.2609178
146 EIF2AK2_ 37383568 8208.30189 0.1806969 0.1597281 0.1628359 0.1635589 0.1631069 0.1639120 0.1688722 0.8839558 0.9345605
38 CCDC85C_ 100069693 125.61538 0.9474747 0.9307531 0.9114478 0.8447430 0.9025301 0.9098232 0.9105894 0.8915731 0.9823513
24 CCDC85C_ 100069585 125.71154 0.9398990 0.8978261 0.8382353 0.8613908 0.8783589 0.8812267 0.8916911 0.8918355 0.9552368
168 HOOK2_2 12876969 41338.60377 0.0311405 0.0296678 0.0307192 0.0328163 0.0278030 0.0282222 0.0285883 0.8928228 1.0538123
167 HOOK2_2 12876987 41339.35849 0.0279196 0.0270365 0.0279717 0.0308079 0.0252206 0.0264513 0.0249635 0.8941228 1.1034512
169 HOOK2_2 12876948 41352.96226 0.0348022 0.0343632 0.0351502 0.0372277 0.0324302 0.0314338 0.0325705 0.9032122 1.0696926
147 EIF2AK2_ 37383588 8208.79245 0.0662880 0.0673229 0.0668573 0.0699649 0.0752748 0.0598727 0.0687655 0.9032206 1.1355713
89 UPK3B_2 76145589 5753.64151 0.3647373 0.3478331 0.3593414 0.3521429 0.3573062 0.3534394 0.3337164 0.9149500 0.9852061
166 HOOK2_2 12876993 41338.73585 0.0275662 0.0268339 0.0284840 0.0302059 0.0257795 0.0252260 0.0276297 0.9151081 1.0957600
150 EIF2AK2_ 37383713 8206.37736 0.0116287 0.0136651 0.0107156 0.0106978 0.0143946 0.0123623 0.0114399 0.9199461 1.2378560
129 HELZ2_ 62199061 2844.77358 0.0132565 0.0153742 0.0122007 0.0152167 0.0161666 0.0211720 0.0152074 0.9203551 1.5970967
37 CCDC85C_ 100069687 125.61538 0.9813131 0.9519357 0.9463095 0.9035486 0.9448893 0.9473016 0.9278222 0.9207546 0.9700631
243 IFI44L_ 79085765 27.94340 0.9017705 0.9406107 0.8635223 0.9056412 0.8500690 0.8492134 0.8333333 0.9241080 1.0430711
32 CCDC85C_ 100069657 125.61538 0.9666667 0.9809297 0.9315745 0.9606593 0.9732967 0.9476061 0.8960040 0.9269007 1.0147549
165 HOOK2_2 12876997 41340.37736 0.0227380 0.0225993 0.0228712 0.0256441 0.0211053 0.0212729 0.0223000 0.9281970 1.1278104
237 IFITM1_ 312434 68.35294 0.9571429 0.9606661 0.8905736 0.9644419 0.9437767 0.9630154 0.9498922 0.9304500 1.0076259
121 HOOK2_ 12877188 21370.73585 0.1143300 0.1066673 0.1141502 0.1131671 0.1096066 0.1130287 0.1156642 0.9329767 1.0116693
23 CCDC85C_ 100069566 125.69231 0.9717172 0.9497206 0.9435224 0.9520768 0.9075720 0.9463099 0.9359238 0.9339879 0.9797880
46 CCDC85C_ 100069724 125.61538 0.9328283 0.8811140 0.8903326 0.8878633 0.9311565 0.8842634 0.8713786 0.9341254 0.9982078
173 HOOK2_2 12876937 41339.18868 0.0319246 0.0313413 0.0317690 0.0336976 0.0299407 0.0304477 0.0304109 0.9378577 1.0555361
238 IFITM1_ 312463 82.53846 0.7617845 0.7555911 0.7150287 0.7559719 0.7477820 0.7495064 0.7905397 0.9386233 1.0377472

6.2 The TH Cell Analysis

Gene POS Avg.Base Normal IFN.a.6 IFN.b.6 IFN.ab.6 IFN.a.12 IFN.b.12 IFN.ab.12 IFN.a.24 IFN.b.24 IFN.ab.24 Min.Fold Max.Fold
235 HLA-DPB1_ 33048602 6509.35849 0.0010416 0.0008355 0.0008486 0.0009521 0.0000760 0.0016394 0.0013623 0.0013274 0.0010804 0.0011045 0.0729386 1.5738292
128 HELZ2_ 62199034 2844.77358 0.0163626 0.0120537 0.0125538 0.0126250 0.0178672 0.0163562 0.0142813 0.0099055 0.0130293 0.0231127 0.6053757 1.4125345
239 IFITM1_ 312518 49.56863 0.1490106 0.1620424 0.2938782 0.2429481 0.0937500 0.1952381 0.2379085 0.2704348 0.1905330 0.2757508 0.6291497 1.9721962
130 HELZ2_ 62199156 2844.43396 0.0149910 0.0126899 0.0096051 0.0132248 0.0144247 0.0119805 0.0119481 0.0115317 0.0102701 0.0102203 0.6407231 0.9622219
150 EIF2AK2_ 37383713 8206.37736 0.0147414 0.0134571 0.0160120 0.0124505 0.0136681 0.0162727 0.0121974 0.0097826 0.0132909 0.0130054 0.6636154 1.1038736
148 EIF2AK2_ 37383623 8218.43396 0.0099360 0.0073559 0.0100664 0.0069197 0.0147517 0.0114611 0.0102307 0.0074173 0.0091063 0.0085628 0.6964240 1.4846702
241 IFI44L_ 79085647 27.94340 0.4957265 0.4563889 0.3761905 0.5109215 0.4450275 0.4936636 0.5121672 0.5092593 0.3478931 0.4920635 0.7017843 1.0331648
132 HELZ2_ 62199190 2844.45283 0.0058042 0.0061712 0.0043537 0.0082894 0.0066653 0.0049752 0.0055615 0.0091815 0.0058678 0.0046162 0.7500990 1.5818638
226 HLA-DPB1_ 33048542 6509.50943 0.0036818 0.0042313 0.0031407 0.0040973 0.0028111 0.0041452 0.0045267 0.0041168 0.0037529 0.0042136 0.7635244 1.2294829
131 HELZ2_ 62199181 2844.35849 0.0100858 0.0101316 0.0120197 0.0092691 0.0132344 0.0087280 0.0141614 0.0079786 0.0127125 0.0095089 0.7910677 1.4040892
49 SMAD3_ 67361773 968.00000 0.0340764 0.0684762 0.0299690 0.0370159 0.2053004 0.0345706 0.0332370 0.0370977 0.0284410 0.0280352 0.8227175 6.0247161
146 EIF2AK2_ 37383568 8208.30189 0.0233245 0.0228477 0.0208581 0.0266197 0.0193369 0.0231148 0.0205561 0.0247085 0.0241278 0.0199855 0.8290384 1.1412748
89 UPK3B_2 76145589 5753.64151 0.0723433 0.0737401 0.0669883 0.0742428 0.0602158 0.0747420 0.0767285 0.0701024 0.0805793 0.0778624 0.8323619 1.1138463
28 CCDC85C_ 100069619 125.88462 0.6422388 0.6427889 0.6304749 0.6358018 0.5948387 0.5456341 0.6416545 0.6532609 0.6545285 0.6332129 0.8495814 1.0191358
214 BRDT_2 92417998 2442.32075 0.6421807 0.5854239 0.6359689 0.6341804 0.5497847 0.6355117 0.6460720 0.6466256 0.6425822 0.6483927 0.8561214 1.0096732
149 EIF2AK2_ 37383679 8206.28302 0.0188665 0.0214736 0.0232734 0.0221736 0.0253922 0.0224347 0.0214525 0.0210027 0.0162439 0.0214373 0.8609952 1.3458881
81 UPK3B_2 76145702 5753.62264 0.0828763 0.0769159 0.0818970 0.0788093 0.0730590 0.0755363 0.0885223 0.0797858 0.0808496 0.0797531 0.8815426 1.0681260
54 COX7A2_2 75953829 5082.01887 0.0344082 0.0387057 0.0373409 0.0323329 0.0306224 0.0366847 0.0385331 0.0384854 0.0339828 0.0390109 0.8899751 1.1337678
238 IFITM1_ 312463 82.53846 0.8557809 0.8126355 0.8547169 0.8645941 0.8173401 0.8581489 0.7791667 0.8078078 0.8193626 0.8890826 0.9104744 1.0389138
243 IFI44L_ 79085765 27.94340 0.8896215 0.9591667 0.9357143 0.8654528 0.8123438 0.8784562 0.9349980 0.9153439 0.8553545 0.9306157 0.9131342 1.0781739
52 SMAD3_ 67361896 968.18868 0.9666215 0.9464186 0.9608842 0.9649444 0.8878476 0.9651946 0.9653679 0.9677906 0.9677688 0.9577458 0.9185060 1.0012095
242 IFI44L_ 79085713 27.94340 0.9819292 1.0000000 0.9523810 0.9360279 0.9855072 0.9677419 0.9825721 0.9021164 0.9833333 0.9457672 0.9187184 1.0184034
59 COX7A2_2 75953960 5081.92453 0.0783989 0.0813104 0.0803097 0.0752622 0.0720848 0.0774212 0.0859859 0.0840107 0.0777620 0.0839639 0.9194620 1.0967749
80 UPK3B_2 76145717 5752.32075 0.2181485 0.2304175 0.2295617 0.2116299 0.2018941 0.2302342 0.2222051 0.2207743 0.2471065 0.2297214 0.9254892 1.1327445
46 CCDC85C_ 100069724 125.61538 0.9138886 0.8868305 0.9168022 0.8958383 0.8505376 0.8937438 0.8830009 0.9029503 0.9068599 0.8988424 0.9306798 1.0031882
147 EIF2AK2_ 37383588 8208.79245 0.0358746 0.0334038 0.0415256 0.0373750 0.0336848 0.0338408 0.0378366 0.0381385 0.0413846 0.0380144 0.9311264 1.1575208
176 HOOK2_2 12876911 41093.18868 0.5373469 0.5025463 0.5548718 0.5384887 0.5493738 0.5457516 0.5586327 0.5581653 0.5548666 0.5538520 0.9352363 1.0396128
83 UPK3B_2 76145689 5765.98113 0.2612200 0.2618450 0.2551548 0.2451893 0.2580878 0.2544979 0.2609420 0.2542030 0.2672785 0.2560899 0.9386311 1.0231930
104 RNF39_ 30039408 767.16981 0.7383827 0.7295692 0.7475960 0.7363309 0.6932901 0.7498446 0.7339636 0.7576127 0.7429396 0.7578557 0.9389306 1.0263726
162 TLR1_ 38805839 487.56604 0.5583725 0.5733711 0.5711377 0.5337995 0.5465214 0.5872620 0.5249235 0.5312232 0.5462176 0.5687931 0.9400955 1.0517387

7 Part VI: The Methylation Status of the Differentially Methylated CpGsites in other autoimmune diseases

7.1 SLE.CD4+ versus SSc.CD4+

Gene Cgsite POS McaM.SSc McoM.SSc Pvalue.SSc FoldChange.SSc McaM.SLE McoM.SLE Pvalue.SLE FoldChange.SLE
317186 EIF2AK2 37383568 37383568 0.1233814 0.1826725 0.0000315 0.6754238 0.1555306 0.3130137 0.0000000 0.4968810
20158 PARP9 122281975 122281975 0.4276390 0.5290290 0.0000693 0.8083470 0.3579342 0.6517962 0.0000000 0.5491504
73006 IFI44L 79085586 79085586 0.6726998 0.7436687 0.0000910 0.9045692 0.4689935 0.7267674 0.0000000 0.6453144
219198 IFITM1 313354 313354 0.2627358 0.3098730 0.0011124 0.8478823 0.4575495 0.4955707 0.0010769 0.9232780
157649 PARP9 122281939 122281939 0.7183252 0.7916144 0.0015986 0.9074181 0.5414367 0.7888373 0.0000000 0.6863731
172157 MX1 42798747 42798747 0.0572312 0.0650165 0.0024990 0.8802565 0.1408137 0.2300620 0.0000000 0.6120683
119415 HELZ2 62199181 62199181 0.0651395 0.0373344 0.0055478 1.7447571 0.2184451 0.1198966 0.0000007 1.8219458
22822 BRDT 92417998 92417998 0.4365022 0.3211686 0.0259938 1.3591063 0.3998090 0.3770251 0.8765567 1.0604310
18023 IFI44L 79085765 79085765 0.4548280 0.4984651 0.0311206 0.9124571 0.2866716 0.4906685 0.0000000 0.5842471
427478 FAM132A 1178246 1178246 0.7422693 0.8213389 0.0357950 0.9037308 0.7160009 0.7586990 0.8705869 0.9437219
59750 BRDT 92414782 92414782 0.7324310 0.7659456 0.0385228 0.9562442 0.7921089 0.7686955 0.0684014 1.0304587

7.2 RA.PBL versus SSc.CD4+

Gene Cgsite POS McaM.SSc McoM.SSc Pvalue.SSc FoldChange.SSc McaM.RA McoM.RA Pvalue.RA FoldChange.RA
194672 EIF2AK2 37383568 37383568 0.1233814 0.1826725 0.0000315 0.6754238 0.1421435 0.1704233 0.0000000 0.8340613
204641 PARP9 122281975 122281975 0.4276390 0.5290290 0.0000693 0.8083470 0.4976405 0.5300614 0.0000000 0.9388356
149108 IFI44L 79085586 79085586 0.6726998 0.7436687 0.0000910 0.9045692 0.4603852 0.5133334 0.0000000 0.8968542
353930 IFITM1 313354 313354 0.2627358 0.3098730 0.0011124 0.8478823 0.6154195 0.5694498 0.0000000 1.0807266
210065 PARP9 122281939 122281939 0.7183252 0.7916144 0.0015986 0.9074181 0.7600392 0.7673751 0.3881497 0.9904403
477689 MX1 42798747 42798747 0.0572312 0.0650165 0.0024990 0.8802565 0.1401662 0.1484040 0.0088041 0.9444910
471312 HELZ2 62199181 62199181 0.0651395 0.0373344 0.0055478 1.7447571 0.0710844 0.0676239 0.0002579 1.0511721
145961 BRDT 92417998 92417998 0.4365022 0.3211686 0.0259938 1.3591063 0.2402171 0.2392868 0.0195615 1.0038875
145476 IFI44L 79085765 79085765 0.4548280 0.4984651 0.0311206 0.9124571 0.1997635 0.2411714 0.0000000 0.8283051
173957 FAM132A 1178246 1178246 0.7422693 0.8213389 0.0357950 0.9037308 0.7583208 0.7458641 0.0000032 1.0167011
148183 BRDT 92414782 92414782 0.7324310 0.7659456 0.0385228 0.9562442 0.8080209 0.7812533 0.0000000 1.0342624

7.3 RA.PBL versus SSc.CD8+

Gene Cgsite POS McaM.SSc McoM.SSc Pvalue.SSc FoldChange.SSc McaM.RA McoM.RA Pvalue.RA FoldChange.RA
204641 PARP9 122281975 122281975 0.4531487 0.5968228 0.0000000 0.7592683 0.4976405 0.5300614 0.0000000 0.9388356
210065 PARP9 122281939 122281939 0.7320359 0.8323341 0.0000001 0.8794977 0.7600392 0.7673751 0.3881497 0.9904403
194672 EIF2AK2 37383568 37383568 0.1373269 0.1882193 0.0000971 0.7296114 0.1421435 0.1704233 0.0000000 0.8340613
471312 HELZ2 62199181 62199181 0.0451481 0.0214664 0.0002035 2.1031944 0.0710844 0.0676239 0.0002579 1.0511721
451067 TTC39C 21572657 21572657 0.1848003 0.1419552 0.0003293 1.3018220 0.7481729 0.6888222 0.0000000 1.0861626
145476 IFI44L 79085765 79085765 0.5151405 0.6067145 0.0011990 0.8490656 0.1997635 0.2411714 0.0000000 0.8283051
449136 TTC39C 21572635 21572635 0.3820672 0.3329965 0.0054331 1.1473609 0.8068542 0.7577563 0.0000000 1.0647938
474109 HELZ2 62199034 62199034 0.1427749 0.0981128 0.0069887 1.4552111 0.1275270 0.1322510 0.2553072 0.9642799
472712 HELZ2 62199156 62199156 0.0221550 0.0106671 0.0071269 2.0769436 0.0818283 0.0769713 0.0000068 1.0631016
472275 HELZ2 62199190 62199190 0.0334972 0.0185647 0.0096154 1.8043459 0.1084547 0.1054170 0.0120716 1.0288165
450014 TTC39C 21572623 21572623 0.3587072 0.3148537 0.0105301 1.1392822 0.7816516 0.7387071 0.0000000 1.0581347
167071 IFI44L 79085713 79085713 0.6866851 0.7410939 0.0116753 0.9265831 0.2537521 0.3171817 0.0000000 0.8000212
47063 RNF39 30039476 30039476 0.3051805 0.3870814 0.0160688 0.7884144 0.1848225 0.1967838 0.0000164 0.9392162
149108 IFI44L 79085586 79085586 0.7097750 0.7625005 0.0178789 0.9308519 0.4603852 0.5133334 0.0000000 0.8968541
46471 RNF39 30039403 30039403 0.4364698 0.5066883 0.0214113 0.8614167 0.2738635 0.3056240 0.0000005 0.8960799
275637 RNF39 30039374 30039374 0.2453951 0.3210745 0.0227590 0.7642931 0.1846558 0.2014602 0.0000081 0.9165874
48849 RNF39 30039466 30039466 0.2398981 0.3018692 0.0269289 0.7947089 0.2981943 0.3105540 0.0000390 0.9602013
47649 RNF39 30039435 30039435 0.4457716 0.5147477 0.0368050 0.8660003 0.2603282 0.2891516 0.0000008 0.9003174
47925 RNF39 30039432 30039432 0.4890092 0.5487349 0.0445974 0.8911575 0.2723385 0.3041660 0.0000004 0.8953613

puweilin

2016-11-17